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Evolution of prevention strategies provides multiple options for managing HIV infection in pregnancy. There is a need to evaluate successes and risks associated with these PMTCT strategies. In a retrospective cohort study, records of mothers who received either of two PMTCT strategies were linked with infant records and analyzed. From a total of 286 paired records, 225 (78.7%) received HAART, 38 (13.3%), Sc-ARVs while 23 (8%) had no ARVs in pregnancy. Overall transmission rate was 2.4% (5/208) in infants from the HAART group and 7.9% (3/38) for the Sc-ARV group. At ninth month of life 1% of infants in the HAART group and 13% in the Sc-ARV group were infected. Four infections occurred in the HAART group after ninth month of life due to breast milk exposure. Factors found to be associated with risk of vertical transmission included duration of ART use 3 months (OR 0.19: 95%CI 0.04-0.90), mixed feeding (OR 3.68: 95%CI 1.01-13.52), HAART in pregnancy (OR 0.07: 95%CI 0.02-0.28) and infant post exposure ARV prophylaxis (OR 0.19: 95%CI 0.05-0.77). Conclusion: HAART is a comparably more efficient PMTCT strategy in improving HIV free survival among exposed infants.