diff --git a/book-example/src/cli/init.md b/book-example/src/cli/init.md
index 43d1ae02d3..8a899afb87 100644
--- a/book-example/src/cli/init.md
+++ b/book-example/src/cli/init.md
@@ -22,7 +22,7 @@ configuration files, etc.
 - The `book` directory is where your book is rendered. All the output is ready to be uploaded
 to a server to be seen by your audience.
 
-- The `SUMMARY.md` file is the most important file, it's the skeleton of your book and is discussed in more detail in another  [chapter](format/summary.html).
+- The `SUMMARY.md` file is the most important file, it's the skeleton of your book and is discussed in more detail in another  [chapter](../format/summary.md)
 
 #### Tip & Trick: Hidden Feature
 When a `SUMMARY.md` file already exists, the `init` command will first parse it and generate the missing files according to the paths used in the `SUMMARY.md`. This allows you to think and create the whole structure of your book and then let mdBook generate it for you.
diff --git a/book-example/src/for_developers/README.md b/book-example/src/for_developers/README.md
index 4f173c904d..ae1069fc8b 100644
--- a/book-example/src/for_developers/README.md
+++ b/book-example/src/for_developers/README.md
@@ -11,8 +11,8 @@ The *For Developers* chapters are here to show you the more advanced usage of
 
 The two main ways a developer can hook into the book's build process is via,
 
-- [Preprocessors](for_developers/preprocessors.html)
-- [Alternate Backends](for_developers/backends.html)
+- [Preprocessors](preprocessors.md)
+- [Alternate Backends](backends.md)
 
 
 ## The Build Process
diff --git a/src/renderer/html_handlebars/hbs_renderer.rs b/src/renderer/html_handlebars/hbs_renderer.rs
index ba5c5e430c..4fad1eeff9 100644
--- a/src/renderer/html_handlebars/hbs_renderer.rs
+++ b/src/renderer/html_handlebars/hbs_renderer.rs
@@ -42,10 +42,6 @@ impl HtmlHandlebars {
                     .to_str()
                     .chain_err(|| "Could not convert path to str")?;
                 let filepath = Path::new(&ch.path).with_extension("html");
-                let filepathstr = filepath
-                    .to_str()
-                    .chain_err(|| "Could not convert HTML path to str")?;
-                let filepathstr = utils::fs::normalize_path(filepathstr);
 
                 // "print.html" is used for the print page.
                 if ch.path == Path::new("print.md") {
@@ -75,10 +71,10 @@ impl HtmlHandlebars {
                 debug!("Render template");
                 let rendered = ctx.handlebars.render("index", &ctx.data)?;
 
-                let rendered = self.post_process(rendered, &filepathstr, &ctx.html_config.playpen);
+                let rendered = self.post_process(rendered, &ctx.html_config.playpen);
 
                 // Write to file
-                debug!("Creating {} ✓", filepathstr);
+                debug!("Creating {} ✓", filepath.display());
                 utils::fs::write_file(&ctx.destination, &filepath, &rendered.into_bytes())?;
 
                 if ctx.is_index {
@@ -120,9 +116,8 @@ impl HtmlHandlebars {
     }
 
     #[cfg_attr(feature = "cargo-clippy", allow(let_and_return))]
-    fn post_process(&self, rendered: String, filepath: &str, playpen_config: &Playpen) -> String {
-        let rendered = build_header_links(&rendered, filepath);
-        let rendered = fix_anchor_links(&rendered, filepath);
+    fn post_process(&self, rendered: String, playpen_config: &Playpen) -> String {
+        let rendered = build_header_links(&rendered);
         let rendered = fix_code_blocks(&rendered);
         let rendered = add_playpen_pre(&rendered, playpen_config);
 
@@ -360,7 +355,7 @@ impl Renderer for HtmlHandlebars {
         debug!("Render template");
         let rendered = handlebars.render("index", &data)?;
 
-        let rendered = self.post_process(rendered, "print.html", &html_config.playpen);
+        let rendered = self.post_process(rendered, &html_config.playpen);
 
         utils::fs::write_file(&destination, "print.html", &rendered.into_bytes())?;
         debug!("Creating print.html ✓");
@@ -497,7 +492,7 @@ fn make_data(
 
 /// Goes through the rendered HTML, making sure all header tags are wrapped in
 /// an anchor so people can link to sections directly.
-fn build_header_links(html: &str, filepath: &str) -> String {
+fn build_header_links(html: &str) -> String {
     let regex = Regex::new(r"<h(\d)>(.*?)</h\d>").unwrap();
     let mut id_counter = HashMap::new();
 
@@ -507,7 +502,7 @@ fn build_header_links(html: &str, filepath: &str) -> String {
                 .parse()
                 .expect("Regex should ensure we only ever get numbers here");
 
-            wrap_header_with_link(level, &caps[2], &mut id_counter, filepath)
+            wrap_header_with_link(level, &caps[2], &mut id_counter)
         })
         .into_owned()
 }
@@ -517,8 +512,7 @@ fn build_header_links(html: &str, filepath: &str) -> String {
 fn wrap_header_with_link(
     level: usize,
     content: &str,
-    id_counter: &mut HashMap<String, usize>,
-    filepath: &str,
+    id_counter: &mut HashMap<String, usize>
 ) -> String {
     let raw_id = utils::id_from_content(content);
 
@@ -532,35 +526,13 @@ fn wrap_header_with_link(
     *id_count += 1;
 
     format!(
-        r##"<a class="header" href="{filepath}#{id}" id="{id}"><h{level}>{text}</h{level}></a>"##,
+        r##"<a class="header" href="#{id}" id="{id}"><h{level}>{text}</h{level}></a>"##,
         level = level,
         id = id,
-        text = content,
-        filepath = filepath
+        text = content
     )
 }
 
-// anchors to the same page (href="#anchor") do not work because of
-// <base href="../"> pointing to the root folder. This function *fixes*
-// that in a very inelegant way
-fn fix_anchor_links(html: &str, filepath: &str) -> String {
-    let regex = Regex::new(r##"<a([^>]+)href="#([^"]+)"([^>]*)>"##).unwrap();
-    regex
-        .replace_all(html, |caps: &Captures| {
-            let before = &caps[1];
-            let anchor = &caps[2];
-            let after = &caps[3];
-
-            format!(
-                "<a{before}href=\"{filepath}#{anchor}\"{after}>",
-                before = before,
-                filepath = filepath,
-                anchor = anchor,
-                after = after
-            )
-        })
-        .into_owned()
-}
 
 // The rust book uses annotations for rustdoc to test code snippets,
 // like the following:
@@ -660,37 +632,32 @@ mod tests {
         let inputs = vec![
             (
                 "blah blah <h1>Foo</h1>",
-                r##"blah blah <a class="header" href="./some_chapter/some_section.html#foo" id="foo"><h1>Foo</h1></a>"##,
+                r##"blah blah <a class="header" href="#foo" id="foo"><h1>Foo</h1></a>"##,
             ),
             (
                 "<h1>Foo</h1>",
-                r##"<a class="header" href="./some_chapter/some_section.html#foo" id="foo"><h1>Foo</h1></a>"##,
+                r##"<a class="header" href="#foo" id="foo"><h1>Foo</h1></a>"##,
             ),
             (
                 "<h3>Foo^bar</h3>",
-                r##"<a class="header" href="./some_chapter/some_section.html#foobar" id="foobar"><h3>Foo^bar</h3></a>"##,
+                r##"<a class="header" href="#foobar" id="foobar"><h3>Foo^bar</h3></a>"##,
             ),
             (
                 "<h4></h4>",
-                r##"<a class="header" href="./some_chapter/some_section.html#" id=""><h4></h4></a>"##,
+                r##"<a class="header" href="#" id=""><h4></h4></a>"##,
             ),
             (
                 "<h4><em>Hï</em></h4>",
-                r##"<a class="header" href="./some_chapter/some_section.html#hï" id="hï"><h4><em>Hï</em></h4></a>"##,
+                r##"<a class="header" href="#hï" id="hï"><h4><em>Hï</em></h4></a>"##,
             ),
             (
                 "<h1>Foo</h1><h3>Foo</h3>",
-                r##"<a class="header" href="./some_chapter/some_section.html#foo" id="foo"><h1>Foo</h1></a><a class="header" href="./some_chapter/some_section.html#foo-1" id="foo-1"><h3>Foo</h3></a>"##,
+                r##"<a class="header" href="#foo" id="foo"><h1>Foo</h1></a><a class="header" href="#foo-1" id="foo-1"><h3>Foo</h3></a>"##,
             ),
         ];
 
         for (src, should_be) in inputs {
-            let filepath = "./some_chapter/some_section.html";
-            let got = build_header_links(&src, filepath);
-            assert_eq!(got, should_be);
-
-            // This is redundant for most cases
-            let got = fix_anchor_links(&got, filepath);
+            let got = build_header_links(&src);
             assert_eq!(got, should_be);
         }
     }
diff --git a/src/renderer/html_handlebars/helpers/navigation.rs b/src/renderer/html_handlebars/helpers/navigation.rs
index 429e3dd3ff..5b8bfddaac 100644
--- a/src/renderer/html_handlebars/helpers/navigation.rs
+++ b/src/renderer/html_handlebars/helpers/navigation.rs
@@ -4,6 +4,8 @@ use std::collections::BTreeMap;
 use serde_json;
 use handlebars::{Context, Handlebars, Helper, RenderContext, RenderError, Renderable};
 
+use utils;
+
 type StringMap = BTreeMap<String, String>;
 
 /// Target for `find_chapter`.
@@ -87,6 +89,13 @@ fn render(
     trace!("Creating BTreeMap to inject in context");
 
     let mut context = BTreeMap::new();
+    let base_path = rc.evaluate_absolute("path", false)?
+                      .as_str()
+                      .ok_or_else(|| RenderError::new("Type error for `path`, string expected"))?
+                      .replace("\"", "");
+
+    context.insert("path_to_root".to_owned(),
+                                json!(utils::fs::path_to_root(&base_path)));
 
     chapter
         .get("name")
diff --git a/src/renderer/html_handlebars/helpers/toc.rs b/src/renderer/html_handlebars/helpers/toc.rs
index f44ea2acab..174ac8272f 100644
--- a/src/renderer/html_handlebars/helpers/toc.rs
+++ b/src/renderer/html_handlebars/helpers/toc.rs
@@ -1,6 +1,8 @@
 use std::path::Path;
 use std::collections::BTreeMap;
 
+use utils;
+
 use serde_json;
 use handlebars::{Handlebars, Helper, HelperDef, RenderContext, RenderError};
 use pulldown_cmark::{html, Event, Parser, Tag};
@@ -77,6 +79,7 @@ impl HelperDef for RenderToc {
                         .replace("\\", "/");
 
                     // Add link
+                    rc.writer.write_all(&utils::fs::path_to_root(&current).as_bytes())?;
                     rc.writer.write_all(tmp.as_bytes())?;
                     rc.writer.write_all(b"\"")?;
 
diff --git a/src/theme/book.js b/src/theme/book.js
index b0d89f33d2..521f137148 100644
--- a/src/theme/book.js
+++ b/src/theme/book.js
@@ -293,9 +293,9 @@ function playpen_text(playpen) {
     var themePopup = document.getElementById('theme-list');
     var themeColorMetaTag = document.querySelector('meta[name="theme-color"]');
     var stylesheets = {
-        ayuHighlight: document.querySelector("[href='ayu-highlight.css']"),
-        tomorrowNight: document.querySelector("[href='tomorrow-night.css']"),
-        highlight: document.querySelector("[href='highlight.css']"),
+        ayuHighlight: document.querySelector("[href$='ayu-highlight.css']"),
+        tomorrowNight: document.querySelector("[href$='tomorrow-night.css']"),
+        highlight: document.querySelector("[href$='highlight.css']"),
     };
 
     function showThemes() {
diff --git a/src/theme/index.hbs b/src/theme/index.hbs
index 0e5fa009a1..45be723a09 100644
--- a/src/theme/index.hbs
+++ b/src/theme/index.hbs
@@ -9,20 +9,18 @@
         <meta name="viewport" content="width=device-width, initial-scale=1">
         <meta name="theme-color" content="#ffffff" />
 
-        <base href="{{ path_to_root }}">
-
-        <link rel="stylesheet" href="book.css">
+        <link rel="stylesheet" href="{{ path_to_root }}book.css">
         <link href="https://fonts.googleapis.com/css?family=Open+Sans:300italic,400italic,600italic,700italic,800italic,400,300,600,700,800" rel="stylesheet" type="text/css">
         <link href="https://fonts.googleapis.com/css?family=Source+Code+Pro:500" rel="stylesheet" type="text/css">
 
         <link rel="shortcut icon" href="{{ favicon }}">
 
         <!-- Font Awesome -->
-        <link rel="stylesheet" href="FontAwesome/css/font-awesome.css">
+        <link rel="stylesheet" href="{{ path_to_root }}FontAwesome/css/font-awesome.css">
 
-        <link rel="stylesheet" href="highlight.css">
-        <link rel="stylesheet" href="tomorrow-night.css">
-        <link rel="stylesheet" href="ayu-highlight.css">
+        <link rel="stylesheet" href="{{ path_to_root }}highlight.css">
+        <link rel="stylesheet" href="{{ path_to_root }}tomorrow-night.css">
+        <link rel="stylesheet" href="{{ path_to_root }}ayu-highlight.css">
 
         <!-- Custom theme stylesheets -->
         {{#each additional_css}}
@@ -107,7 +105,7 @@
                         <h1 class="menu-title">{{ book_title }}</h1> 
 
                         <div class="right-buttons">
-                            <a href="print.html" title="Print this book" aria-label="Print this book">
+                            <a href="{{ path_to_root }}print.html" title="Print this book" aria-label="Print this book">
                                 <i id="print-button" class="fa fa-print"></i>
                             </a>
                         </div>
@@ -144,13 +142,13 @@
                     <nav class="nav-wrapper" aria-label="Page navigation">
                         <!-- Mobile navigation buttons -->
                         {{#previous}}
-                            <a rel="prev" href="{{link}}" class="mobile-nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
+                            <a rel="prev" href="{{ path_to_root }}{{link}}" class="mobile-nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
                                 <i class="fa fa-angle-left"></i>
                             </a>
                         {{/previous}}
 
                         {{#next}}
-                            <a rel="next" href="{{link}}" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
+                            <a rel="next" href="{{ path_to_root }}{{link}}" class="mobile-nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
                                 <i class="fa fa-angle-right"></i>
                             </a>
                         {{/next}}
@@ -162,13 +160,13 @@
 
             <nav class="nav-wide-wrapper" aria-label="Page navigation">
                 {{#previous}}
-                    <a href="{{link}}" class="nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
+                    <a href="{{ path_to_root }}{{link}}" class="nav-chapters previous" title="Previous chapter" aria-label="Previous chapter" aria-keyshortcuts="Left">
                         <i class="fa fa-angle-left"></i>
                     </a>
                 {{/previous}}
 
                 {{#next}}
-                    <a href="{{link}}" class="nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
+                    <a href="{{ path_to_root }}{{link}}" class="nav-chapters next" title="Next chapter" aria-label="Next chapter" aria-keyshortcuts="Right">
                         <i class="fa fa-angle-right"></i>
                     </a>
                 {{/next}}
@@ -213,29 +211,32 @@
         {{/if}}
 
         {{#if playpen_js}}
-        <script src="ace.js" type="text/javascript" charset="utf-8"></script>
-        <script src="editor.js" type="text/javascript" charset="utf-8"></script>
-        <script src="mode-rust.js" type="text/javascript" charset="utf-8"></script>
-        <script src="theme-dawn.js" type="text/javascript" charset="utf-8"></script>
-        <script src="theme-tomorrow_night.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}ace.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}editor.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}mode-rust.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}theme-dawn.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}theme-tomorrow_night.js" type="text/javascript" charset="utf-8"></script>
         {{/if}}
 
         {{#if search_enabled}}
-        <script src="searchindex.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}searchindex.js" type="text/javascript" charset="utf-8"></script>
+        <script>
+            var path_to_root = "{{path_to_root}}";
+        </script>
         {{/if}}
         {{#if search_js}}
-        <script src="elasticlunr.min.js" type="text/javascript" charset="utf-8"></script>
-        <script src="mark.min.js" type="text/javascript" charset="utf-8"></script>
-        <script src="searcher.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}elasticlunr.min.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}mark.min.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}searcher.js" type="text/javascript" charset="utf-8"></script>
         {{/if}}
 
-        <script src="clipboard.min.js" type="text/javascript" charset="utf-8"></script>
-        <script src="highlight.js" type="text/javascript" charset="utf-8"></script>
-        <script src="book.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}clipboard.min.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}highlight.js" type="text/javascript" charset="utf-8"></script>
+        <script src="{{ path_to_root }}book.js" type="text/javascript" charset="utf-8"></script>
 
         <!-- Custom JS scripts -->
         {{#each additional_js}}
-        <script type="text/javascript" src="{{this}}"></script>
+        <script type="text/javascript" src="{{ path_to_root }}{{this}}"></script>
         {{/each}}
 
         {{#if is_print}}
diff --git a/src/theme/searcher/searcher.js b/src/theme/searcher/searcher.js
index 63958f991c..32080bcd79 100644
--- a/src/theme/searcher/searcher.js
+++ b/src/theme/searcher/searcher.js
@@ -9,7 +9,14 @@ window.search = window.search || {};
     if (!Mark || !elasticlunr) {
         return;
     }
-    
+
+    //IE 11 Compatibility from https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/String/startsWith
+    if (!String.prototype.startsWith) {
+        String.prototype.startsWith = function(search, pos) {
+            return this.substr(!pos || pos < 0 ? 0 : +pos, search.length) === search;
+        };
+    }
+
     var search_wrap = document.getElementById('search-wrapper'),
         searchbar = document.getElementById('searchbar'),
         searchbar_outer = document.getElementById('searchbar-outer'),
@@ -137,7 +144,7 @@ window.search = window.search || {};
             url.push("");
         }
 
-        return '<a href="' + url[0] + '?' + URL_MARK_PARAM + '=' + searchterms + '#' + url[1]
+        return '<a href="' + path_to_root + url[0] + '?' + URL_MARK_PARAM + '=' + searchterms + '#' + url[1]
             + '" aria-details="teaser_' + teaser_count + '">' + result.doc.breadcrumbs + '</a>'
             + '<span class="teaser" id="teaser_' + teaser_count + '" aria-label="Search Result Teaser">' 
             + teaser + '</span>';
diff --git a/src/utils/mod.rs b/src/utils/mod.rs
index 56e0f00483..567b49387e 100644
--- a/src/utils/mod.rs
+++ b/src/utils/mod.rs
@@ -68,6 +68,35 @@ pub fn id_from_content(content: &str) -> String {
     normalize_id(trimmed)
 }
 
+fn adjust_links(event: Event) -> Event {
+
+    lazy_static! {
+        static ref HTTP_LINK: Regex = Regex::new("^https?://").unwrap();
+        static ref MD_LINK: Regex = Regex::new("(?P<link>.*).md(?P<anchor>#.*)?").unwrap();
+    }
+
+    match event {
+        Event::Start(Tag::Link(dest, title)) => {
+            if !HTTP_LINK.is_match(&dest) {
+                if let Some(caps) = MD_LINK.captures(&dest) {
+
+                    let mut html_link = [&caps["link"], ".html"].concat();
+
+                    if let Some(anchor) = caps.name("anchor") {
+                        html_link.push_str(anchor.as_str());
+                    }
+
+                    return Event::Start(Tag::Link(Cow::from(html_link), title))
+                }
+            }
+
+            Event::Start(Tag::Link(dest, title))
+        },
+        _ => event
+    }
+
+}
+
 /// Wrapper around the pulldown-cmark parser for rendering markdown to HTML.
 pub fn render_markdown(text: &str, curly_quotes: bool) -> String {
     let mut s = String::with_capacity(text.len() * 3 / 2);
@@ -79,6 +108,7 @@ pub fn render_markdown(text: &str, curly_quotes: bool) -> String {
     let p = Parser::new_ext(text, opts);
     let mut converter = EventQuoteConverter::new(curly_quotes);
     let events = p.map(clean_codeblock_headers)
+                  .map(adjust_links)
                   .map(|event| converter.convert(event));
 
     html::push_html(&mut s, events);
@@ -177,6 +207,17 @@ mod tests {
     mod render_markdown {
         use super::super::render_markdown;
 
+        #[test]
+        fn preserves_external_links() {
+           assert_eq!(render_markdown("[example](https://www.rust-lang.org/)", false), "<p><a href=\"https://www.rust-lang.org/\">example</a></p>\n");
+        }
+
+        #[test]
+        fn it_can_adjust_markdown_links() {
+            assert_eq!(render_markdown("[example](example.md)", false), "<p><a href=\"example.html\">example</a></p>\n");
+            assert_eq!(render_markdown("[example_anchor](example.md#anchor)", false), "<p><a href=\"example.html#anchor\">example_anchor</a></p>\n");
+        }
+
         #[test]
         fn it_can_keep_quotes_straight() {
             assert_eq!(render_markdown("'one'", false), "<p>'one'</p>\n");
diff --git a/tests/rendered_output.rs b/tests/rendered_output.rs
index a95fe96e7d..a6549ed0ab 100644
--- a/tests/rendered_output.rs
+++ b/tests/rendered_output.rs
@@ -83,12 +83,11 @@ fn check_correct_cross_links_in_nested_dir() {
 
     let first = temp.path().join("book").join("first");
     let links = vec![
-        r#"<base href="../">"#,
-        r#"href="intro.html""#,
-        r#"href="first/index.html""#,
-        r#"href="first/nested.html""#,
-        r#"href="second.html""#,
-        r#"href="conclusion.html""#,
+        r#"href="../intro.html""#,
+        r#"href="../first/index.html""#,
+        r#"href="../first/nested.html""#,
+        r#"href="../second.html""#,
+        r#"href="../conclusion.html""#,
     ];
 
     let files_in_nested_dir = vec!["index.html", "nested.html"];
@@ -100,14 +99,14 @@ fn check_correct_cross_links_in_nested_dir() {
     assert_contains_strings(
         first.join("index.html"),
         &[
-            r##"href="first/index.html#some-section" id="some-section""##,
+            r##"href="#some-section" id="some-section""##,
         ],
     );
 
     assert_contains_strings(
         first.join("nested.html"),
         &[
-            r##"href="first/nested.html#some-section" id="some-section""##,
+            r##"href="#some-section" id="some-section""##,
         ],
     );
 }
@@ -367,8 +366,8 @@ fn by_default_mdbook_use_index_preprocessor_to_convert_readme_to_index() {
         .join("first")
         .join("index.html");
     let expected_strings = vec![
-        r#"href="first/index.html""#,
-        r#"href="second/index.html""#,
+        r#"href="../first/index.html""#,
+        r#"href="../second/index.html""#,
         "First README",
     ];
     assert_contains_strings(&first_index, &expected_strings);