The goal of this study was to determine the prevalence of bacterial vaginosis (BV) in Peruvian women from socioeconomically deprived populations and to determine the association between BV and risk factors for sexually transmitted diseases (STDs). Women were administered an epidemiologic survey to determine sexual risk behaviour and they provided biological samples to test for BV and STDs. The prevalence of BV was high (27%) and was significantly associated with having a bacterial STD or trichomoniasis. Age, marital status, and a history of sex work, but not of sexual experience, frequency of intercourse, and unprotected intercourse, were associated with BV. As BV may be a marker for STDs, screening for STDs should be performed in individuals with BV to promote early detection and treatment of co-infecting sexually transmitted pathogens.