Abstract Background The burden of malnutrition among HIV-infected children is not well described in sub-Saharan Africa, even though it is an important problem to take into account to guarantee appropriate healthcare for these children. We assessed the prevalence of malnutrition and its associated factors among HIV-infected children in HIV care programmes in Central and West-Africa. Methods A cross-sectional study was conducted from September to December 2011 among the active files of HIV-infected children aged 2–19 years old, enrolled in HIV-care programmes supported by the Sidaction Growing Up Programme in Benin, Burundi, Cameroon, Côte d’Ivoire, Mali, Chad and Togo. Socio-demographics characteristics, anthropometric, clinical data, and nutritional support were collected. Anthropometric indicators, expressed in Z-scores, were used to define malnutrition: Height-for-age (HAZ), Weight-for-Height (WHZ) for children