Objective: To compare etiologies of prolonged amenorrhea in a cohort of HIV-infected women with a cohort of similar uninfected at-risk women. Materials and Methods: Women from the Women's Interagency HIV Study were seen every 6 months, and completed surveys including questions about their menstruation. Those who reported no vaginal bleeding for at least 1 year ("prolonged amenorrhea") with subsequent resumption of bleeding were compared with women in whom bleeding had stopped permanently ("menopause"). Characteristics associated with reversible prolonged amenorrhea were ascertained. Results: Of 828 women with prolonged amenorrhea, 37.6% had reversible amenorrhea and 62.4% never resumed menses. HIV-seropositive women with prolonged amenorrhea were significantly younger at cessation of menses than HIV-negative women (p < 0.0001). Of those with reversible prolonged amenorrhea, approximately half were taking medications associated with amenorrhea, including 95 (30.6%) hormonal contraception, 80 (25.7%) opiates/stimulants, 16 (5.1%) psychotropic medications, and 6 (1.9%) chemotherapy. HIV-seropositive women were less likely to have medications as a cause of amenorrhea than seronegative women (p = 0.02). In multivariable analysis, women with reversible prolonged amenorrhea of unknown etiology were younger (p < 0.0001), more often obese (p = 0.03), and less educated (p = 0.01) than those with permanent amenorrhea. Among HIV-seropositive women, markers of severe immunosuppression were not associated with prolonged amenorrhea. Conclusion: Women with HIV infection have unexplained prolonged amenorrhea more often than at-risk seronegative women. This is especially common among obese, less-educated women. Prolonged amenorrhea in the HIV-seropositive women should be evaluated and not be presumed to be to the result of menopause.