Eliminating of paediatric HIV within prevention of mother to child transmission (PMTCT) interventions rests on complete follow-up of all children. We report on predictors of child attrition in the PMTCT cascade over 5 years where 1050 pregnant women were enrolled at 36 gestational weeks. Mother and child pairs were followed up at birth, 6 weeks, 4 months, 9 months, and every 6 months thereafter for 60 months. Higher attrition was observed for children of economically advantaged, socially stable mothers regardless of HIV status, whereas compliance was observed for children whose mothers tested positive for HIV-1, HSV-2 and Syphilis. Low birthweight was associated with attrition regardless of maternal HIV status. Five years predictors of attrition did not differ by maternal HIV status, as HIV-exposed children succumbed to mortality and those not exposed were loss to follow-up (LFU). Child follow-up is influenced more by maternal lifestyle and health risks leading to retention of high-risk children in PMTCT programmes.