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To describe prevalence and risk factors for wasting and stunting among HIV-infected children with a median duration of 3 years of antiretroviral therapy (ART) at the time of their enrollment in the cohort study.Wasting and stunting at ART initiation and enrollment were defined as weight-for-height/body mass index-for-age Z scores < −2 and height-for-age Z scores < −2, respectively. Logistic regression was used to assess risk factors for wasting and stunting. Main predictive factors were age at enrollment, nutritional status and age (< or ≥5 years) at ART initiation and ART duration (< or ≥3 years on first-line, or ≥3 years including a switch to second-line ART).Two hundred forty-four children 2–16 years of age were enrolled. Overall, wasting and stunting prevalence dropped off consistently in children 2–10 years of age, between ART initiation and enrollment, while it remained at high levels, 52% and 42%, respectively, in children 10–16 years of age. Risk factors for wasting at enrollment were ART duration of ≥3 years including a switch to second-line [adjusted odds ratio (aOR): 3.9, 95% confidence interval (CI): 1.7–8.9] and wasting at ART initiation (aOR: 2.7, 95% CI: 1.4–5.2). The risk factor for stunting at enrollment was stunting at ART initiation (aOR: 11.6, 95% CI: 5.4–25.0), independent of ART duration.Malnutrition at the time of ART initiation was the main predictor of malnutrition at enrollment among HIV-infected children on ART. Longer duration on ART had no overall protective effect on wasting and stunting. Growth and virologic monitoring are of utmost importance in the comprehensive care of children with HIV infection.