Prevention of mother-to-child transmission (PMTCT) is essential in HIV/AIDS control. We analysed 2000-05 data from mother-infant pairs in our PMTCT programme in rural Uganda, examining programme utilization and outcomes, HIV transmission rates and predictors of death or loss to follow-up (LFU). Out of 19,017 women, 1,037 (5.5%) attending antenatal care services tested HIV positive. Of these, 517 (50%) enrolled in the PMTCT programme and gave birth to 567 infants. Before tracing, 303 (53%) mother-infant pairs were LFU. Reasons for dropout were infant death and lack of understanding of importance of follow-up. Risk of death or LFU was higher among infants with no or incomplete intrapartum prophylaxis (OR = 1.90, 95% CI 1.07-3.36) and of weaning age <6 months (OR 2.55, 95% CI 1.42-4.58), and lower in infants with diagnosed acute illness (OR 0.30, 95% CI 0.16-0.55). Mother-to-child HIV cumulative transmission rate was 8.3%, and 15.5% when HIV-related deaths were considered. Improved tracking of HIV-exposed infants is needed in PMTCT programmes where access to early infant diagnosis is still limited.