A Google Webmaster Help thread asks, can Google read links in Flash files or JavaScript? The simple answer is yes, they can. But it is not that simple.

Some people want to know the answer to this question because they want to know if their content will be indexed or not. Some want the links in those files to be found, while some don’t. In fact, years ago, if you did not want a search engine to crawl a link, typically a duplicate content page, you would use JavaScript. Now, you are no longer safe, you must nofollow the link or noindex those duplicate pages or take other action.

The thing is, Google won’t always crawl links in JavaScript or Flash either. So if you want your links to be found, be safe and put them in standard html format. But if you don’t want your links to be found, putting them in JavaScript or Flash won’t guarantee that.

Top contributor, Webado said:

JohnMu of Google confirmed that post.

As you can see, in this case, your damned if you do and damned if you don’t.

Forum discussion at Google Webmaster Help.