Management of Human Immunodeficiency Virus infection remains a major challenge in many sub-Saharan African countries. Antiretroviral drugs which have reduced significantly the mortality rate of this pandemic disease are a source of side effects. Among these side effects, adult lipodystrophy has already been described by several authors. The aim of this study is to determine the prevalence of lipodystrophy and associate factors in children on antiretroviral therapy, managed at Charles De Gaulle Children University Hospital and Yalgado Ouedrago University Hospital in Ouagadougou, Burkina Faso. This is a cross-sectional study conducted from June 2013 to January 2014. We included children aged 2 to 15 years who had been on antiretroviral treatment for at least six months with no severe acute malnutrition (wasting). Lipodystrophy was diagnosed clinically after assessment of morphological changes. Overall, 323 children complying with the inclusion criteria were examined. The average duration of antiretroviral therapy was 5.3 years. Forty five children had lipodystrophy, i.e. 13.9% prevalence rate. One hundred and twenty seven different lipodystrophic lesions were noted, hence 82.7% lipoatrophy and 17.3% lipohypertrophy. The most common presentations were: face (32%), lower limbs (26%) and upper limbs (15.7%). Factors associated with lipoatrophy were: age above 10 years (P = 0.004); male gender (P = 0.0004); antiretroviral treatment duration of more than 60 months (P < 0.001) and treatment with stavudine (P = 0.01). Our study showed that lipodystrophy is not exceptional in children on antiretroviral therapy in Ouagadougou. However, more researches on lipid profiles of these children are necessary to prevent other common complications related to fat accumulation.