Background Sexually transmitted diseases (STDs) are increasing among gay, bisexual, and other men who have sex with men (MSM). Little is known about the use of websites and mobile phone applications to meet sexual partners ("hookup sites") and association with STD diagnoses. Methods We performed a demographic and behavioral assessment of 415 MSM presenting to the Rhode Island STD clinic. Bivariate and multivariable analyses assessed associations between using hookup sites and testing positive for syphilis, gonorrhea, or chlamydia. Venue-based affiliation networks were created to evaluate hookup sites and their association with STD diagnoses. Results Among 415 MSM, 78% reported meeting a partner online in the last 12 months, and 25% tested positive for at least one STD. Men who met partners online were more likely to be white (67% vs. 54%, P = 0.03) and have more than 10 lifetime partners (87% vs. 58%, P < 0.05). The most commonly used hookup sites included Grindr (78%), Scruff (35%), and Tinder (22%). In the multivariable analysis, only Scruff use was associated with testing positive for an STD (odds ratio, 2.28; 95% confidence interval, 1.09-4.94). However, among men who met partners online, 75% of men diagnosed as having an STD had met a sexual partner on Grindr, including 100% of those who were diagnosed as having gonorrhea. Conclusions Use of hookup sites was nearly ubiquitous among MSM undergoing STD screening. Specific hookup sites were significantly associated with STD diagnoses among MSM. Greater efforts are needed to promote STD screening and prevention among MSM who meet partners online.