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Objective: The objective of this study is to estimate per-contact probability of HIV transmission in homosexual men due to unprotected anal intercourse (UAI) in the era of HAART. Design: Data were collected from a longitudinal cohort study of community-based HIV-negative homosexual men in Sydney, Australia. Methods: A total of 1427 participants were recruited from June 2001 to December 2004. They were followed up with 6-monthly detailed behavioral interviews and annual testing for HIV till June 2007. Data were used in a bootstrapping method, coupled with a statistical analysis that optimized a likelihood function for estimating the per-exposure risks of HIV transmission due to various forms of UAI. Results: During the study, 53 HIV seroconversion cases were identified. The estimated per-contact probability of HIV transmission for receptive UAI was 1.43% [95% confidence interval (CI) 0.48–2.85] if ejaculation occurred inside the rectum, and it was 0.65% (95% CI 0.15–1.53) if withdrawal prior to ejaculation was involved. The estimated transmission rate for insertive UAI in participants who were circumcised was 0.11% (95% CI 0.02–0.24), and it was 0.62% (95% CI 0.07–1.68) in uncircumcised men. Thus, receptive UAI with ejaculation was found to be approximately twice as risky as receptive UAI with withdrawal or insertive UAI for uncircumcised men and over 10 times as risky as insertive UAI for circumcised men. Conclusion: Despite the fact that a high proportion of HIV-infected men are on antiretroviral treatment and have undetectable viral load, the per-contact probability of HIV transmission due to UAI is similar to estimates reported from developed country settings in the pre-HAART era.