Different religious narratives associate same-sex sexuality, in its various manifestations, with moral deviation or sin. Gay men who are socialized in more religious communities appear to experience and internalize greater levels of homonegativity, as well as to present greater indicators of depressive symptoms. The purpose of this study was to evaluate indicators of perceived homonegativity in the community and internalized, and signs/symptoms of depression reported by Brazilian gay men with a nominal religion and compare them to those reported by Atheists or Agnostics. Our sample comprised 194 Brazilian gay men, distributed into three groups: Christians (Protestants and Catholics, n = 71; 36.6%); Spiritualists (Kardecists or religions of African origin, n = 52; 26.8%) and Atheists or Agnostics (n = 71; 36.6%). The following measurement instruments were used: sociodemographic questionnaire, Internalized Homophobia Scale and Beck Depression Scale. High mean scores of depression were verified in all groups, and 60% of the sample presented some level of depression. There was a higher level of self-reported homonegativity among Christians and Spiritualists compared to that reported by Atheists or Agnostics, with the differences between the groups being significant. The regression analysis indicated a significant effect of religion on homonegativity, but not on depression. Our results suggest that gay men's chronic exposure to non-affirming religious affiliation contexts may harm the construction of a positive gay identity and should be taken into consideration when addressing mental health inequalities of sexual minorities.