diff --git a/cmd/thanos/sidecar.go b/cmd/thanos/sidecar.go
index e58e6779dd..fd00fbe177 100644
--- a/cmd/thanos/sidecar.go
+++ b/cmd/thanos/sidecar.go
@@ -229,7 +229,7 @@ func runSidecar(
 				return nil
 			})
 			if err != nil {
-				return errors.Wrap(err, "buildinfo query")
+				return errors.Wrap(err, "failed to get prometheus version")
 			}
 			return nil
 		}, func(error) {
diff --git a/pkg/store/prometheus.go b/pkg/store/prometheus.go
index 37f7b369dd..b1bf61e65e 100644
--- a/pkg/store/prometheus.go
+++ b/pkg/store/prometheus.go
@@ -520,11 +520,17 @@ func (p *PrometheusStore) LabelValues(ctx context.Context, r *storepb.LabelValue
 		if err != nil {
 			return nil, err
 		}
+
+		// using set to handle duplicate values.
+		labelValuesSet := make(map[string]struct{})
 		for _, s := range sers {
 			if val, exists := s[r.Label]; exists {
-				vals = append(vals, val)
+				labelValuesSet[val] = struct{}{}
 			}
 		}
+		for key := range labelValuesSet {
+			vals = append(vals, key)
+		}
 	}
 	sort.Strings(vals)
 	return &storepb.LabelValuesResponse{Values: vals}, nil