Adolescents and young adults are at high risk of human immunodeficiency virus (HIV) infection in sub-Saharan Africa. Previous reports have found that university students in Africa comprise a sexually active population, although the prevalence of HIV or sexually transmitted infections (STI) has not been measured. We conducted a cross-sectional survey of students from five large universities in Kampala, Uganda, using respondent-driven sampling. We asked students to complete behavioral questionnaires and provide biological samples to test for HIV, Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, Trichomonas vaginalis, and bacterial vaginosis. We enrolled 649 students and obtained interpretable data from 640. Around 50% of the respondents were male, and the mean age was 22 years. An estimated 0.8% (95% CI 0.0-2.0) of male students had Chlamydia infection, approximately 4.3% (95% CI 2.0-7.0) had syphilis, 0.4% (95% CI 0.0-0.9) had HIV, and none had gonorrhea. An estimated 32.6% (95% CI 22.4-40.8) of women had bacterial vaginosis, 2.5% (95% CI 0.7-6.3) had Chlamydia infection, 1.7% (95% CI 0.5-3.6) had syphilis, 1.0% (95% CI 0.0-2.4) had gonorrhea, 0.9% (95% CI 0.0-4.2) had trichomoniasis, and 0.9% (95% CI 0.0-1.8) had HIV. We found no significant risk factors for HIV or other STI among males. We also found that not using a condom during the latest sexual intercourse was significantly associated with HIV infection, other STI, or bacterial vaginosis (OR 2.16; 95% 1.26-3.78) among females. We conclude that while university students are sexually active and there is substantial risk for syphilis, there is little evidence of substantially increased HIV risk among them.