BACKGROUND: Early growth of HIV-exposed, uninfected (HEU) children is poorer than that of their HIV-unexposed, uninfected (HUU) counterparts but there is little longitudinal or longer term information about the growth effects of early HIV exposure. METHODS: We performed a longitudinal analysis to compare growth of HEU and HUU infants and children using data from two cohort studies in Lusaka, Zambia. Initially 207 HUU and 200 HEU infants from the Breastfeeding and Postpartum Health (BFPH) study and 580 HUU and 165 HEU from the Chilenje Infant Growth, Nutrition and Infection Study (CIGNIS) had anthropometric measurements taken during infancy and again when school-aged, at which time 66 BFPH children and 326 CIGNIS children were available. We analysed the data from the two cohorts separately using linear mixed models. Linear regression models were used as a secondary analysis at the later time points, adjusting for breastfeeding duration. We explored when the main group differences in growth emerged in order to estimate the largest 'effect periods'. RESULTS: After adjusting for socioeconomic status and maternal education, HEU children had lower weight-for-age, length-for-age and BMI-for-age Z-scores during early growth and these differences still existed when children were school-aged. Exposure group differences changed most between 1 and 6 weeks and between 18 months and ~7.5 years. CONCLUSIONS: HEU children have poorer early growth than HUU children which persists into later growth. Interventions to improve growth of HEU children need to target pregnant women and infants.