There are several potential structural issues that could be preventing a website from ranking well in search engines, even if on-page SEO best practices have been implemented. These include pages not being properly indexed, canonicalization issues, lack of incoming links, missing or improperly configured XML sitemap, site speed issues, use of Flash, and text displayed as images rather than HTML. The document provides steps to test for each issue and suggestions for how to discuss findings with one's web developer.