Antiretroviral therapy (ART) improves growth and survival of HIV-infected individuals. We designed a retrospective cohort study to assess clinical factors associated with growth in HIV-infected children on ART in Uganda between July 2003 and March 2006. Height and weight measurements taken pre- and post-ART initiation for at least 6 months were age- and gender-standardized to CDC 2000 reference. We analyzed medical records of 749 children receiving ART. Descriptive and logistic regression analyses were conducted to identify covariates associated with risk of either stunting or being underweight. Longitudinal regression analysis with a mixed model using autoregressive covariance structure was used to compare change in height and weight before and after initiation of ART. The mean age of the study population at first visit was 7.5 years. Mean height-for-age, weight-for-age, and weight-for-height percentiles at first visit were 8.6, 7.7, and 7.9, respectively. At last visit mean height-for-age, weight-for-age, and weight-for-height percentiles were 8.6, 13.3, and 13.8, respectively. Baseline weight-for-age z score of 1 or more was protective against stunting (odds ratio [OR] 0.25, confidence interval [CI] 0.18-0.35) while baseline height-for-age z score of 1 or more was protective against becoming underweight (OR 0.75, CI 0.63-0.88). Children in World Health Organization (WHO) stages II, III, and IV at baseline were 1.5 times more likely to become underweight (OR 1.51, CI 1.07-2.14). Initiation of ART resulted in improvement in mean standardized weight-for-age z score and weight-for-age percentiles (p < 0.001). Weight-for-age percentile and z score improved significantly after initiation of ART. This pediatric population gained weight more rapidly than height after initiation of ART.