I added the following to my `.emacs`. The hook is to convert tabs to spaces to avoid unpleasant surprises with code blocks. For source to ska-untabify see the EmacsWiki

    (autoload 'markdown-mode "markdown-mode")
    (add-to-list 'auto-mode-alist '("\\.mdwn" . markdown-mode))

    (add-hook 'markdown-mode-hook
               '(lambda ()
                   (make-local-hook 'write-contents-hooks)
                    (add-hook 'write-contents-hooks 'ska-untabify nil t)))

;; [[DavidBremner]]