Hello: I have Cider and Clojure Mode installed from Elpa, with Org mode fresh from Git as of today (May 9, 2015). I've provided files below to replicate a bug in babel fontification behavior, having to do with which order things are loaded in.
If you save the files below, and run emacs -Q -l ~/.emacs-config test.org then you will see a message about an "org-mode fontification error". If you edit the .emacs-config file, moving the line (add-to-list 'load-path "~/org-mode/lisp/") to before the (require 'cider) line, then you don't see the error and fontification behavior is as expected. == test.org ==================================================================== #+BEGIN_SRC emacs-lisp (defun foo () 0) #+END_SRC #+BEGIN_SRC clojure (defn bar [] (fn [x] 1)) #+END_SRC ================================================================================ == .emacs-config =============================================================== (when (>= emacs-major-version 24) (require 'package) (package-initialize) (add-to-list 'package-archives '("melpa" . "http://melpa.milkbox.net/packages/") t) ) (require 'cider) (require 'clojure-mode) ;; Problematic line (add-to-list 'load-path "~/org-mode/lisp/") (require 'org) (org-babel-do-load-languages 'org-babel-load-languages '((clojure . t) (emacs-lisp . t))) (require 'ob-clojure) (setq org-babel-clojure-backend 'cider) (setq org-src-fontify-natively t) ================================================================================ Emacs : GNU Emacs 25.0.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 3.12.2) of 2015-04-14 on Teacup Package: Org-mode version 8.2.10 (release_8.2.10 @ /home/joe/org-mode/lisp/)