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Late HIV diagnosis is associated with higher medical costs, early mortality among individuals, and HIV transmission in the population. Even under optimal configurations of stable or declining HIV incidence and increase in HIV case findings, no change in proportion of late HIV diagnosis is projected after year 2019. We investigated the association among social capital, gender, and late HIV diagnosis.We conduct ecological analyses (ZIP code, N = 166) using negative binomial regression of gender-specific rates of late HIV diagnoses (an AIDS defining illness or a CD4 count ≤200 cell/μL within 12 months of a new HIV diagnosis) in 2005 and 2006 obtained from the New York City HIV Surveillance Registry, and social capital indicators (civic engagement, political participation, social cohesion, and informal social control) from the New York Social Indicators Survey, 2004.Overall, low to high political participation and social cohesion corresponded with significant (P < 0.0001) decreasing trends in late HIV diagnosis rates. Among men [relative risk (RR) = 0.66, 95% CI: (0.47 to 0.98)] and women [RR = 0.43, 95% CI: (0.28 to 0.67)], highest political participation was associated with lower relative odds of late HIV diagnosis, independent of income inequality. Highest informal social control [RR = 0.67, 95% CI: (0.48 to 0.93)] among men only and moderate social cohesion [RR = 0.71, 95% CI: (0.55 to 0.92)] among women only were associated with the outcome adjusting for social fragmentation, income inequality, and racial composition.The magnitude of association between social capital and late HIV diagnosis varies by gender and by social capital indicator.