http://apiwiki.twitter.com/REST%20API%20Documentation#AccountMethods

update_profile_colors
Sets one or more hex values that control the color scheme of the authenticating user's profile page on twitter.com.  These values are also returned in the /users/show API method.
URL: http://twitter.com/account/update_profile_colors.format
Formats: xml, json
Method(s): POST
Parameters: one or more of the following parameters must be present.  Each parameter's value must be a valid hexidecimal value, and may be either three or six characters (ex: #fff or #ffffff).
• profile_background_color.  Optional.
• profile_text_color.  Optional.
• profile_link_color.  Optional.
• profile_sidebar_fill_color.  Optional.
• profile_sidebar_border_color.  Optional.