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Background Post-partum loss to follow-up and lack of early HIV infant diagnosis (EID) can significantly affect the efficiency of programs for the prevention of mother-to-child transmission. Methods In a prospective observational study 167 women were enrolled at week 36 of gestation and followed with their infants up to one year after delivery. Retention was defined as the proportion of women who attended the 12 months visit and EID as an HIV PCR test performed within 2 months. Determinants for retention and EID were assessed in univariate analyses and in multivariable logistic regression models. Results Women lost to follow-up (24/167 or 14.4%) had a shorter duration of antiretroviral therapy (ART) at enrolment in comparison to women retained in care ( p = 0.025). Lack of EID (occurring in 18.9% of the cases) was directly correlated, although not significantly, with a history of child death ( p = 0.071), a higher educational level ( p = 0.083), and female infant gender ( p = 0.064). Conclusions Longer duration of ART at enrolment significantly predicted a better post-partum retention, suggesting that specific counselling interventions should be targeted to recent ART initiators. A low proportion of infants did not receive an EID, but predictive factors were difficult to identify.