Denmark is currently experiencing the highest immigration rate in its modern history. Population surveys indicate that negative public attitudes toward immigrants actually stem from attitudes toward their (perceived) Islamic affiliation. We used a framing paradigm to investigate the explicit and implicit attitudes of Christian and Atheist Danes toward targets framed as Muslims or as immigrants. The results showed that explicit and implicit attitudes were more negative when the target was framed as a Muslim, rather than as an immigrant. Interestingly, implicit attitudes were qualified by the participants' religion. Specifically, analyses revealed that Christians demonstrated more negative implicit attitudes toward immigrants than Muslims. Conversely, Atheists demonstrated more negative implicit attitudes toward Muslims than Atheists. These results suggest a complex relationship between religion, and implicit and explicit prejudice. Both the religious affiliation of the perceiver and the perceived religious affiliation of the target are key factors in social perception.