The objective of this study was to determine extent of HIV conspiracy belief endorsement among men who have sex with men (MSM) in Pretoria, and assess whether endorsement of HIV conspiracy beliefs are associated with inconsistent condom use and never testing for HIV. A cross-sectional survey using respondent-driven sampling was conducted between February and August 2009. A high proportion of respondents endorsed HIV conspiracy beliefs. MSM commonly endorsed beliefs related to AIDS information being held back from the general public (51.0%), HIV being a man-made virus (25.5%), and people being used as guinea pigs in HIV research and with HIV treatments (approximately 20%). Bisexually- or heterosexually-identified MSM were significantly more likely to endorse conspiracy beliefs compared to homosexually-identified MSM (38.5% vs. 14.7%). Endorsing conspiracy beliefs was not associated with unprotected anal intercourse; however, it was significantly associated with not having been HIV tested (AOR: 2.4; 95% CI: 1.1-5.7). Endorsing beliefs in HIV conspiracies reflects a mistrust in government institutions and systems which could be an impediment to seeking HIV-related services, including HIV counseling and testing.