Common themes are separation of church and state, science and religion, dissemination of freethought, and applied philosophy.

In Free Inquiry's April–May 2006 issue, the magazine published four of the cartoons that had originally appeared in the Danish newspaper Jyllands-Posten and that had sparked violent worldwide Muslim protests.

Kurtz, editor-in-chief of Free Inquiry said, "What is at stake is the precious right of freedom of expression".

The Borders refused to carry this issue in their main and Waldenbooks stores because of the cartoons.

[6] The "blogosphere" widely condemned the decision of Borders to ban the magazine[7] and columnist Christopher Hitchens lamented the action in an article.