diff --git a/codox/resources/codox/theme/default/css/default.css b/codox/resources/codox/theme/default/css/default.css
index 33f78fed..b48c5cbc 100644
--- a/codox/resources/codox/theme/default/css/default.css
+++ b/codox/resources/codox/theme/default/css/default.css
@@ -44,7 +44,7 @@ h5.license {
     right: 0;
     height: 22px;
     color: #f5f5f5;
-    padding: 5px 7px;
+    padding: 7px 10px;
 }
 
 #content {
@@ -92,16 +92,17 @@ h5.license {
 
 #header {
     background: #3f3f3f;
-    box-shadow: 0 0 8px rgba(0, 0, 0, 0.4);
+    border-bottom: 1px solid #cccccc;
     z-index: 100;
 }
 
 #header h1 {
+    display: block;
+    float: left;
     margin: 0;
     padding: 0;
     font-size: 18px;
     font-weight: lighter;
-    text-shadow: -1px -1px 0px #333;
 }
 
 #header h1 .project-version {
@@ -121,6 +122,27 @@ h5.license {
     color: #f5f5f5;
 }
 
+#langs {
+    display: block;
+    float: left;
+    font-size: 16px;
+    margin: 0 10px;
+    font-weight: lighter;
+}
+
+#langs .lang {
+    display: inline-block;
+    margin: 0 2px;
+    padding: 0 7px;
+    background-color: #bbb;
+    border-radius: 6px;
+    vertical-align: middle;
+}
+
+#langs .lang.current {
+    background-color: #a33;
+}
+
 .sidebar a {
     color: #333;
 }
@@ -325,7 +347,8 @@ h5.license {
 h4.type,
 h4.dynamic,
 h4.added,
-h4.deprecated {
+h4.deprecated,
+h4.lang {
     float: left;
     margin: 3px 10px 15px 0;
     font-size: 15px;
@@ -336,7 +359,8 @@ h4.deprecated {
 .public h4.type,
 .public h4.dynamic,
 .public h4.added,
-.public h4.deprecated {
+.public h4.deprecated,
+.public h4.lang {
     font-size: 13px;
     font-weight: bold;
     margin: 3px 0 0 10px;
@@ -344,7 +368,8 @@ h4.deprecated {
 
 .members h4.type,
 .members h4.added,
-.members h4.deprecated {
+.members h4.deprecated,
+.members h4.lang {
     margin-top: 1px;
 }
 
@@ -364,6 +389,16 @@ h4.deprecated {
     color: #880000;
 }
 
+.public h4.lang, .public h4.lang a {
+    font-weight: normal;
+    font-variant: normal;
+    color: #717171;
+}
+
+.public h4.lang.current {
+    color: #a33;
+}
+
 .namespace {
     margin-bottom: 30px;
 }
diff --git a/codox/src/codox/main.clj b/codox/src/codox/main.clj
index 1a11ab30..9f3cb953 100644
--- a/codox/src/codox/main.clj
+++ b/codox/src/codox/main.clj
@@ -4,6 +4,7 @@
   (:require [clojure.string :as str]
             [clojure.java.shell :as shell]
             [codox.reader.clojure :as clj]
+            [codox.reader.clojurescript :as cljs]
             [codox.reader.plaintext :as text]))
 
 (defn- writer [{:keys [writer]}]
@@ -19,29 +20,9 @@
       (throw
          (Exception. (str "Could not resolve codox writer " writer-sym))))))
 
-(defn- macro? [var]
-  (= (:type var) :macro))
-
-(defn- read-macro-namespaces [paths read-opts]
-  (->> (clj/read-namespaces paths read-opts)
-       (map (fn [ns] (update-in ns [:publics] #(filter macro? %))))
-       (remove (comp empty? :publics))))
-
-(defn- merge-namespaces [namespaces]
-  (for [[name namespaces] (group-by :name namespaces)]
-    (assoc (first namespaces) :publics (mapcat :publics namespaces))))
-
-(defn- cljs-read-namespaces [paths read-opts]
-  ;; require is here to allow Clojure 1.3 and 1.4 when not using ClojureScript
-  (require 'codox.reader.clojurescript)
-  (let [reader (find-var 'codox.reader.clojurescript/read-namespaces)]
-    (merge-namespaces
-     (concat (reader paths read-opts)
-             (read-macro-namespaces paths read-opts)))))
-
 (def ^:private namespace-readers
   {:clojure       clj/read-namespaces
-   :clojurescript cljs-read-namespaces})
+   :clojurescript cljs/read-namespaces})
 
 (defn- var-symbol [namespace var]
   (symbol (name (:name namespace)) (name (:name var))))
@@ -77,14 +58,49 @@
     (filter #(some (partial ns-matches? %) ns-filters) namespaces)
     namespaces))
 
+(defn- cross-platform?
+  "Do given options indicate *both* Clojure and ClojureScript sources?"
+  [{:keys [language] :as opts}]
+  (= language :both))
+
 (defn- read-namespaces
+  "Returns {<language> <namespace-seq>} for cross-platform opts,
+  or <namespace-seq> otherwise."
   [{:keys [language root-path source-paths namespaces metadata exclude-vars] :as opts}]
-  (let [reader (namespace-readers language)]
-    (-> (reader source-paths (select-keys opts [:exception-handler]))
-        (filter-namespaces namespaces)
-        (remove-excluded-vars exclude-vars)
-        (add-source-paths root-path source-paths)
-        (add-ns-defaults metadata))))
+  (if (cross-platform? opts)
+    {:clojure       (read-namespaces (assoc opts :language :clojure))
+     :clojurescript (read-namespaces (assoc opts :language :clojurescript))}
+    (let [reader (namespace-readers language)]
+      (-> (reader source-paths (select-keys opts [:exception-handler]))
+          (filter-namespaces namespaces)
+          (remove-excluded-vars exclude-vars)
+          (add-source-paths root-path source-paths)
+          (add-ns-defaults metadata)))))
+
+(defn- get-var-langs
+  "Returns {<ns> {<var> <set-of-languages>}} for given namespaces."
+  ([language namespaces var-langs]
+   (reduce
+     (fn [var-langs ns]
+       (reduce
+         (fn [var-langs public-var]
+           (update-in var-langs [(:name ns) (:name public-var)]
+             #(conj (or % #{}) language)))
+         var-langs
+         (:publics ns)))
+     var-langs
+     namespaces))
+
+  ([options namespaces]
+   (if-not (cross-platform? options)
+     (get-var-langs (:language options) namespaces {})
+     (->>
+       (get-var-langs :clojure (:clojure namespaces) {})
+       (get-var-langs :clojurescript (:clojurescript namespaces))))))
+
+(comment (get-var-langs {:language :clojure}
+           '({:name codox.main :publics ({:name defaults} {:name bar})}
+             {:name codox.foo  :publics ({:name bar})})))
 
 (defn- read-documents [{:keys [doc-paths doc-files] :or {doc-files :all}}]
   (cond
@@ -121,7 +137,10 @@
      (let [options    (merge defaults options)
            write-fn   (writer options)
            namespaces (read-namespaces options)
-           documents  (read-documents options)]
+           documents  (read-documents options)
+           var-langs  (get-var-langs options namespaces)]
        (write-fn (assoc options
                         :namespaces namespaces
-                        :documents  documents)))))
+                        :documents  documents
+                        :var-langs  var-langs
+                        :cross-platform? (cross-platform? options))))))
diff --git a/codox/src/codox/reader/clojure.clj b/codox/src/codox/reader/clojure.clj
index f37346c0..119f2e80 100644
--- a/codox/src/codox/reader/clojure.clj
+++ b/codox/src/codox/reader/clojure.clj
@@ -116,8 +116,8 @@
 
 (defn- find-namespaces [file]
   (cond
-    (.isDirectory file) (ns/find-namespaces-in-dir file)
-    (jar-file? file)    (ns/find-namespaces-in-jarfile (JarFile. file))))
+    (.isDirectory file) (set (ns/find-namespaces-in-dir file))
+    (jar-file? file)    (set (ns/find-namespaces-in-jarfile (JarFile. file)))))
 
 (defn read-namespaces
   "Read Clojure namespaces from a set of source directories (defaults
diff --git a/codox/src/codox/reader/clojurescript.clj b/codox/src/codox/reader/clojurescript.clj
index dee1892c..1db1296f 100644
--- a/codox/src/codox/reader/clojurescript.clj
+++ b/codox/src/codox/reader/clojurescript.clj
@@ -4,6 +4,8 @@
   (:require [clojure.java.io :as io]
             [cljs.analyzer :as an]
             [cljs.analyzer.api :as ana]
+            [cljs.closure]
+            [cljs.env]
             [clojure.string :as str]))
 
 (defn- cljs-filename? [filename]
@@ -15,7 +17,7 @@
        (-> file .getName cljs-filename?)))
 
 (defn- remove-quote [x]
-  (if (and (list? x) (= (first x) 'quote))
+  (if (and (seq? x) (= (first x) 'quote))
     (second x)
     x))
 
@@ -50,15 +52,16 @@
    :else                   :var))
 
 (defn- read-var [file vars var]
-  (-> var
-      (select-keys [:name :line :arglists :doc :dynamic :added :deprecated :doc/format])
-      (update-some :name (comp symbol name))
-      (update-some :arglists remove-quote)
-      (update-some :doc correct-indent)
-      (assoc-some  :file    (.getPath file)
-                   :type    (var-type var)
-                   :members (map (partial read-var file vars)
-                                 (protocol-methods var vars)))))
+  (let [vt (var-type var)]
+    (-> var
+        (select-keys [:name :line :arglists :doc :dynamic :added :deprecated :doc/format])
+        (update-some :name (comp symbol name))
+        (update-some :arglists remove-quote)
+        (update-some :doc correct-indent)
+        (assoc-some  :file    (if (= vt :macro) (:file var) (.getPath file))
+                     :type    vt
+                     :members (map (partial read-var file vars)
+                                   (protocol-methods var vars))))))
 
 (defn- read-publics [state namespace file]
   (let [vars (vals (ana/ns-publics state namespace))]
@@ -70,10 +73,11 @@
          (sort-by (comp str/lower-case :name)))))
 
 (defn- analyze-file [file]
-  (let [state (ana/empty-state)]
-    (binding [an/*analyze-deps* false]
-      (ana/no-warn
-        (ana/analyze-file state file {})))
+  (let [opts  (cljs.closure/add-implicit-options {})
+        state (cljs.env/default-compiler-env opts)]
+    (ana/no-warn
+     (cljs.closure/validate-opts opts)
+     (ana/analyze-file state file opts))
     state))
 
 (defn- read-file [path file exception-handler]
diff --git a/codox/src/codox/writer/html.clj b/codox/src/codox/writer/html.clj
index 0a4f9c81..efad384d 100644
--- a/codox/src/codox/writer/html.clj
+++ b/codox/src/codox/writer/html.clj
@@ -146,8 +146,27 @@
    (if-let [doc (:doc metadata)]
      (markdown-to-html doc project ns))])
 
+(defn- language-fileext
+  ([language]
+   (case language
+     :clojure       ".clj"
+     :clojurescript ".cljs"
+     nil            ""))
+  ([language base-language]
+   (when (not= language base-language)
+     (language-fileext language))))
+
+(defn- index-filename [language]
+  (str "index" (language-fileext language) ".html"))
+
 (defn- ns-filename [namespace]
-  (str (:name namespace) ".html"))
+  (str (:name namespace)
+    (language-fileext (:language namespace) (:base-language namespace))
+    ".html"))
+
+(comment
+  (ns-filename {:name 'my-ns :language :clojure})
+  (ns-filename {:name 'my-ns :language :clojure :base-language :clojure}))
 
 (defn- ns-filepath [output-dir namespace]
   (str output-dir "/" (ns-filename namespace)))
@@ -235,11 +254,12 @@
        [:span.bottom]])))
 
 (defn- index-link [project on-index?]
-  (list
-   [:h3.no-link [:span.inner "Project"]]
-   [:ul.index-link
-    [:li.depth-1 {:class (if on-index? "current")}
-     (link-to "index.html" [:div.inner "Index"])]]))
+  (when-not (:cross-platform? project)
+    (list
+      [:h3.no-link [:span.inner "Project"]]
+      [:ul.index-link
+       [:li.depth-1 {:class (if on-index? "current")}
+        (link-to "index.html" [:div.inner "Index"])]])))
 
 (defn- topics-menu [project current-doc]
   (if-let [docs (seq (:documents project))]
@@ -275,16 +295,26 @@
     (get-in project [:html :namespace-list] default)))
 
 (defn- namespaces-menu [project current-ns]
-  (let [namespaces (:namespaces project)]
+  (when (:show-namespaces? project)
+    (let [namespaces (:namespaces project)]
+      (list
+        [:h3.no-link [:span.inner "Namespaces"]]
+        (case (namespace-list-type project)
+          :flat   (flat-namespaces namespaces current-ns)
+          :nested (nested-namespaces namespaces current-ns))))))
+
+(defn- platforms-menu [project]
+  (when (:show-platforms? project)
     (list
-     [:h3.no-link [:span.inner "Namespaces"]]
-     (case (namespace-list-type project)
-       :flat   (flat-namespaces namespaces current-ns)
-       :nested (nested-namespaces namespaces current-ns)))))
+      [:h3.no-link [:span.inner "Platforms"]]
+      [:ul.index-link
+       [:li.depth-1 (link-to (index-filename :clojure) [:div.inner "Clojure"])]
+       [:li.depth-1 (link-to (index-filename :clojure) [:div.inner "ClojureScript"])]])))
 
 (defn- primary-sidebar [project & [current]]
   [:div.sidebar.primary
    (index-link project (nil? current))
+   (platforms-menu project)
    (topics-menu project current)
    (namespaces-menu project current)])
 
@@ -314,10 +344,23 @@
    [:span.project-name (h (:name project))] " "
    [:span.project-version (h (:version project))]])
 
+(defn- header-platforms [project]
+  (when (:cross-platform? project)
+    (let [{:keys [language]} project]
+      [:div#langs
+       (if (= language :clojure)
+         [:div.lang.current "clj"]
+         [:div.lang (link-to (index-filename :clojure) "clj")])
+
+       (if (= language :clojurescript)
+         [:div.lang.current "cljs"]
+         [:div.lang (link-to (index-filename :clojurescript) "cljs")])])))
+
 (defn- header [project]
   [:div#header
    [:h2 "Generated by " (link-to "https://github.com/weavejester/codox" "Codox")]
-   [:h1 (link-to "index.html" (project-title project))]])
+   [:h1 (link-to "index.html" (project-title project))]
+   (header-platforms project)])
 
 (defn- package [project]
   (if-let [p (:package project)]
@@ -360,16 +403,28 @@
         [:ul.topics
          (for [doc docs]
            [:li (link-to (doc-filename doc) (h (:title doc)))])]))
-     [:h2 "Namespaces"]
-     (for [namespace (sort-by :name (:namespaces project))]
-       [:div.namespace
-        [:h3 (link-to (ns-filename namespace) (h (:name namespace)))]
-        [:div.doc (format-docstring project nil (update-in namespace [:doc] util/summary))]
-        [:div.index
-         [:p "Public variables and functions:"]
-         (unordered-list
-          (for [var (sorted-public-vars namespace)]
-            (list " " (link-to (var-uri namespace var) (h (:name var))) " ")))]])]]))
+
+     (when (:show-platforms? project)
+       (list
+         [:h2 "Platforms"]
+         [:p "This project includes both Clojure and ClojureScript code, please "
+          [:strong "choose a platform"] " to view its documentation:"]
+         [:ul
+          [:li (link-to (index-filename :clojure)       "Clojure")]
+          [:li (link-to (index-filename :clojurescript) "ClojureScript")]]))
+
+     (when (:show-namespaces? project)
+       (list
+         [:h2 "Namespaces"]
+         (for [namespace (sort-by :name (:namespaces project))]
+           [:div.namespace
+            [:h3 (link-to (ns-filename namespace) (h (:name namespace)))]
+            [:div.doc (format-docstring project nil (update-in namespace [:doc] util/summary))]
+            [:div.index
+             [:p "Public variables and functions:"]
+             (unordered-list
+               (for [var (sorted-public-vars namespace)]
+                 (list " " (link-to (var-uri namespace var) (h (:name var))) " ")))]])))]]))
 
 (defmulti format-document
   "Format a document into HTML."
@@ -425,6 +480,24 @@
      [:h4.type (name (:type var))])
    (if (:dynamic var)
      [:h4.dynamic "dynamic"])
+
+   (if (:cross-platform? project)
+     (let [languages (get-in project [:var-langs (:name namespace) (:name var)])
+           has-clj? (contains? languages :clojure)
+           has-cljs? (contains? languages :clojurescript)
+           {:keys [language]} project]
+
+       (list
+         (when has-clj?
+           (if (= language :clojurescript)
+             [:h4.lang (link-to (var-uri (assoc namespace :language :clojure) var) "clj")]
+             [:h4.lang.current "clj"]))
+
+         (when has-cljs?
+           (if (= language :clojure)
+             [:h4.lang (link-to (var-uri (assoc namespace :language :clojurescript) var) "cljs")]
+             [:h4.lang.current "cljs"])))))
+
    (added-and-deprecated-docs var)
    (if (:type-sig var)
      [:div.type-sig
@@ -464,13 +537,62 @@
   (doseq [dir dirs]
     (.mkdirs (io/file output-dir dir))))
 
+(defn- cross-platform-namespaces
+  [namespaces language base-language]
+  (map
+    #(assoc %
+       :language language
+       :base-language base-language)
+    (get namespaces language)))
+
 (defn- write-index [output-dir project]
-  (spit (io/file output-dir "index.html") (transform-html project (index-page project))))
+  (let [{:keys [namespaces cross-platform?]} project]
+
+    (when cross-platform?
+      ;; Write an index file for each language
+      (doseq [language (keys namespaces)]
+        (let [namespaces (cross-platform-namespaces namespaces language
+                           (:base-language project))
+              project
+              (assoc project
+                :namespaces namespaces
+                :language   language
+                :show-platforms?  false
+                :show-namespaces? true)]
+          (spit (io/file output-dir (index-filename language))
+            (transform-html project (index-page project))))))
+
+    ;; Always write a main index file
+    (let [project (assoc project
+                    :show-platforms?  cross-platform?
+                    :show-namespaces? (not cross-platform?))]
+      (spit (io/file output-dir (index-filename nil))
+        (transform-html project (index-page project))))))
 
 (defn- write-namespaces [output-dir project]
-  (doseq [namespace (:namespaces project)]
-    (spit (ns-filepath output-dir namespace)
-          (transform-html project (namespace-page project namespace)))))
+  (let [{:keys [namespaces cross-platform?]} project]
+
+    (if cross-platform?
+      ;; Write namespace files for each language
+      (doseq [language (keys namespaces)]
+        (let [namespaces (cross-platform-namespaces namespaces language
+                           (:base-language project))]
+          (doseq [namespace namespaces]
+            (let [project (assoc project
+                            :namespaces namespaces
+                            :language   language
+                            :show-platforms?  false
+                            :show-namespaces? true)]
+              (spit (ns-filepath output-dir namespace)
+                (transform-html project (namespace-page project namespace)))))))
+
+      ;; Write namespace files for only language
+      (doseq [namespace namespaces]
+        (let [project (assoc project
+                        :show-platforms? false
+                        :show-namespaces? true)]
+          (spit (ns-filepath output-dir namespace)
+            (transform-html project (namespace-page project namespace))))))))
 
 (defn- write-documents [output-dir project]
   (doseq [document (:documents project)]