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To estimate new human immunodeficiency virus (HIV) diagnosis rates among HIV negative men who have sex with men (MSM) who are repeatedly tested for HIV in sexually transmitted disease (STD) clinics and assess the impact of demographic and disease-specific characteristics that are associated with higher HIV diagnosis rates.Retrospective analysis using 2010 to 2013 data from the STD Surveillance Network (SSuN), a sentinel surveillance system comprised of health departments in 12 cities conducting sentinel surveillance in 40 STD clinics. We analyzed data from all MSM repeatedly (≥2 times) tested for HIV, with an initial negative HIV test required for staggered cohort entry. Follow-up time was accrued from the date of the first negative HIV test to the most recent negative test or the first positive HIV test. The STD diagnoses during the follow-up period were reviewed. We estimated HIV diagnoses rates (number of HIV diagnoses/total number of person-years [PY] at risk) by demographic and clinical characteristics with 95% confidence intervals (CI) using an inverse variance weighted random effects model, adjusting for heterogeneity between SSuN jurisdictions.Overall, 640 HIV diagnoses occurred among 14,824 individuals and 20,951.6 PY of observation, for an adjusted incidence of HIV diagnosis of 3.0 per 100 PY (95% CI, 2.6–3.4). Rates varied across race/ethnicity groups with the highest rate among Blacks (4.7/100 PY; 95% CI, 4.1–5.3) followed by Hispanics, whites, and persons of other races/ethnicities. Men who have sex with men having a diagnosis of primary or secondary (P&S) syphilis on or after the first negative HIV test had a higher new HIV diagnosis rate (7.2/100 PY; 95% CI, 5.8–9.0) compared with MSM who did not have a P&S syphilis diagnosis (2.8/100 PY; 95% CI, 2.6–3.1). Men who have sex with men who tested positive for rectal gonorrhea (6.3/100 PY; 95% CI, 5.7–6.9) or rectal chlamydia (5.6/100 PY; 95% CI, 4.6–6.6) had higher rates of new HIV diagnosis when compared to those with negative test results.Men who have sex with men attending SSuN STD clinics have high rates of new HIV diagnoses, particularly those with a previous diagnosis of P&S syphilis, rectal chlamydia, and/or gonorrhea. Sexually transmitted disease clinics continue to be important clinical setting for diagnosing HIV among MSM populations.