Objective To examine how the associations of specific religious affiliations with recent suicidal ideation vary by sexual orientation among young adults. Method This project was a cross-sectional secondary analysis of data from the 2006 and 2011 surveys of the National Research Consortium of Counseling Centers in Higher Education. The analytic sample was restricted to persons between the ages of 18–29 (n = 40,150). Multiple logistic regression analyses were used to examine associations of religious affiliations with recent suicidal ideation between heterosexual and sexual minority (e.g., gay, lesbian, bisexual, questioning) young adults. Results Approximately 6.7% of the sample self-identified as sexual minority. Compared to heterosexuals, sexual minorities were more likely to report recent suicidal ideation (aOR = 4.52, 95% CI = 3.97–5.16). Among heterosexuals, Unspecified Christian and Catholic denominations were associated with 24% and 37% reduced odds of recent suicidal ideation compared to agnostic/atheist heterosexuals. However, among sexual minorities, Unspecified Christian and Catholic denominations were associated with 68% and 77% increased odds of recent suicidal ideation compared to agnostic/atheist sexual minorities. Unspecified Christian and Catholic sexual minorities had 184% and 198% increased odds of recent suicidal ideation compared to Unitarian/Universalist sexual minorities. Conclusions Although protective for heterosexuals, religious affiliation may not be globally protective against suicidal ideation among sexual minorities.