BackgroundPoor retention in HIV care of mother-baby pairs remains a public health challenge in the elimination of mother-to-child transmission (eMTCT) of HIV. We determined the rate of non-retention and time to non-retention of mother-baby pairs and associated factors in Gulu district, Northern Uganda.MethodsMother-baby pairs enrolled into the eMTCT programme at Gulu Regional Referral Hospital (GRRH) and Lacor Hospital (LH) were retrospectively followed for 18 months. The primary outcomes were the rate of non-retention and time to non-retention of mother-baby pairs in HIV care. Data were abstracted from the antiretroviral treatment and early infant diagnosis (EID) registers, and mother/baby appointment books at the health facilities. Additional data on possible reasons for non-retention were obtained from cross-sectional interviews of mothers. Time to non-retention was calculated as the duration between enrolment of mother-baby pair into care and the date when the mother and/or baby missed a scheduled visit and did not return within 30 days. Factors associated with time to non-retention were assessed using Cox proportional hazards regression analysis. The measures of association were expressed as hazards ratio (HR) with 95% confidence intervals. Alpha was set at 0.05. The adjusted analysis includes variables with p <0.2 in the bivariable analysis or considered potential confounders. The Analysis used Stata version 12.ResultsA total of 410 mother-baby pairs were enrolled in this study. Overall, non-retention by 18 month was 30.5%; higher at GRRH (34.7%) than LH (25.8%), p = 0.049. Non-retention was higher among pairs where the infant had no EID, adjusted (adj) HR = 5.81; 95% CI (2.55, 13.24), non-disclosure of mother’s HIV status, adj.HR = 1.86; 95% CI (1.22, 2.85), and lack of privacy during counselling session, adj.HR = 1.86; 95% CI (1.26, 2.85). Non-retention was about 60% lower [adj.HR = 0.43; 95% CI (0.20, 0.92)] among pairs where the mothers understood and appreciated the importance of adhering to all clinic appointments together with the baby.ConclusionNearly a third of mother-baby pairs are not retained in HIV care. Lack of EID services, poor quality service, non-disclosure of mother’s HIV status, and understanding the importance of adhering to all appointments together with the baby, were associated with time to non-retention.