This is another hot potato. It is known by everybody that pure HTML is powerless to make complex sites with a lot of functionality (anyway, HTML was not intended to be a programming languages for building Web applications, so nobody expects that you can use HTML to handle writing to a database or even for storing session information) as required by today's Web users and that is why other programming languages (like JavaScript, or PHP) come to enhance HTML. For now search engines just ignore JavaScript they encounter on a page. As a result of this, first if you have links that are inside the JavaScript code, chances are that they will not be spidered. Second, if JavaScript is in the HTML file itself (rather than in an external .js file that is invoked when necessary) this clutters the html file itself and spiders might just skip it and move to the next site. Just for your information, there is a <noscript> tag that allows to provide alternative to running the script in the browser but because most of its applications are pretty complicated, it is hardly suitable to explain it here.