Objective To determine the prevalence of bacterial vaginosis in the HIV/AIDS patients of primary health care clinics in Jos Plateau state, Nigeria. Methods Female genital swabs were collected from primary health care centers, Jos and analyzed by microscopy, culture, etc. in Jos University Teaching Hospital from December 2006 to December 2007. Data on epidemiologic indices were collected, using structured interviewer-administered questionnaires. Results The incidence of bacterial vaginosis in the study was 28% ( n=196/700). Among the HIV/AIDS group, the bacterial vaginosis incidence was 36% ( n=126/350), while in the control (non-HIV patients) group, the rate was 20% (70/350) with a statistically significant difference at 95 percent confidence level ( P<0.05). HIV/AIDS and non-HIV (control) patients contributed 64% ( n=126/196) and 36% ( n=70/196), respectively. The risks to bacterial vaginosis included vaginal douching with disinfectant/detergent constituted (60%), poor use of condom 40%, a median age of 26 years, and a median number of 3 sex partners per week. Conclusions There was a significant statistical difference in prevalence of bacterial vaginosis between the HIV/AIDS group and non-HIV(control) group of patients in the study. Risk behaviors that promote the incidence of bacterial vaginosis should be especially paid attention.