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Introduction A number of studies have linked Highly Active Antiretroviral Therapy (HAART) to adverse pregnancy outcome but the mechanism is not well understood. Hypothesis This study postulated abnormal vaginal flora (AVF) as the link between HAART and adverse pregnancy outcome. Objective The study was designed to determine correlates of AVF with special emphasis on the association between AVF and HAART in HIV-1 positive pregnant women on HAART in Kisumu, Kenya. Method This cross sectional study was carried out at Lumumba sub county hospital. The facility receive patients from Kisumu county and its surrounding; a region with high HIV and BV prevalence plus high maternal and neonatal morbidities and mortalities. Willing 76 pregnant women who started HAART on or before first trimester were enrolled after signing informed consent forms. Using formatted questionnaire participants were interviewed on demographic, clinical and behavioral information. The samples were collected in second trimester and BV determined by Nugent’s criteria. Fisher Exact Chi square test and multinomial logistic regression was used to determine the association of HAART and participants characteristics with AVF. Results Vaginal douching any time earlier than two weeks to specimen collection [9.67(1.03-90.41)] and non efavirenz based HAART [24.57(2.39-253.14)] were positively associated with BV and intermediate vaginal flora respectively while self-employment [0.06(0.01-0.88)] and one sexual partner in the last two months [0.13(0.02-0.70)] being negatively associated with intermediate vaginal flora. Meanwhile non efavirenz based HAART [17.10(1.18-247.34)] and vaginal douching anytime earlier than two weeks to specimen collection [12.70(1.10-146.)] had independent positive association with intermediate vaginal flora and BV respectively. Conclusion This study found a positive independent association between HAART and intermediate vaginal flora. Similar to BV, it has been discovered that intermediate vaginal flora is linked to poor pregnancy outcome. This study has therefore proved that HAART alters vaginal flora leading to adverse pregnancy outcome.