Check the Formatting Configuration in your Theme Options Panel. By default, WordPress® comes with several Formatting Filters built into its publishing system. Advanced users may find them annoying, particularly if you already know XHTML and you're not using the Visual Editor for WordPress®. These Formatting Filters include: wpautop, balanceTags, wptexturize, convert_chars & convert_smilies. The most important Filter is wpautop. It converts double line-breaks in your content into paragraphs (<p>...</p>). The other Filters, well, they do a few different things, but for the most part, they're responsible for keeping your code clean, handling XHTML entity conversions for special characters like ampersands, and balancing the overall structure of your code. All of that being said, if you plan to write your own XHTML, without the assistance of the Visual Editor, you can safely disable these Filters to prevent your raw code from being modified by them.
Broken Content: If you've already created Posts/Pages using the Visual Editor for WordPress®, disabling these Filters can cause your existing content to appear broken. For example, the wpautop filter converts double line-breaks in your content into paragraphs (<p>...</p>). So, if you've already published a lot of content that depends on automatic paragraphs, and then you disable wpautop, your content will become jumbled. Just keep this in mind if you disable these Filters, and then find your content in a mess. It is easy to think your theme is to blame, when actually it is just these Filters at work, or not at work. In either case, the problem will be temporary, not permanent. To correct the issue, adjust your configuration. I've attached a screenshot.
