Increasingly, faith-based organisations are being asked to participate in HIV prevention and care activities. This paper presents formative research on HIV/AIDS prevention messages, activities and policies within six religious institutions in Cross River State, Nigeria, at urban and rural sites. Data collection methods included a review of written HIV policies gathered from national church and mosque offices and 48 key informant interviews. The study highlights differences in messages between mainstream and Pentecostal Christians and Muslims. Although all groups stated a core message of abstinence outside marriage and faithfulness within marriage, Pentecostal churches tended to have more messages of punishment and condemnation for people infected with HIV. Urban churches/mosques tended to have more HIV resources and programmes. Attitudes towards condom use varied by denomination and individual; although few saw a role for religious institutions to promote condoms there were exceptions voiced. These findings indicate that religious organisations are already playing a role in HIV prevention but their responses are not uniform. Public health organisations and policy-makers should be aware of these denominational differences as they engage with religious institutions and leaders in HIV prevention and care.