We examined the association between amphetamine use and HIV incidence for 2991 men who have sex with men (MSM) who tested anonymously for HIV in San Francisco. HIV incidence among 290 amphetamine users was 6.3% per year (95% CI 1.9-10.6%), compared with 2.1% per year (95% CI 1.3-2.9%) among 2701 non-users (RR 3.0, 95% CI 1.4-6.5). HIV prevention programmes in San Francisco should include efforts to reduce amphetamine use and associated high-risk sexual behaviors.