BACKGROUND: There is limited information about malnutrition, growth evolution and metabolic changes among children initiated early on lopinavir-based antiretroviral therapy (ART) in Africa. METHODS: HIV-1-infected children, age <2 years were initiated on ART, as part of the MONOD ANRS 12206 project, conducted in Burkina Faso and Cote d'Ivoire. Weight-for-age, height-for-age and weight-for-height Z-scores (WAZ, HAZ, WHZ) defined malnutrition (Z-score <-2 standard deviations [SD]) using WHO growth references. Biological data were collected every 6 months. Factors associated with baseline malnutrition were evaluated using multivariate logistic regression, and with growth evolution in the first 24 months on ART using linear mixed models. RESULTS: Between 2011 and 2013, 161 children were enrolled: 64% were from Abidjan, 54% were girls. At ART initiation, median age was 13.7 months [IQR 7.7; 18.4], 52% were underweight (WAZ), 52% were stunted (HAZ), and 36% were wasted (WHZ). Overall, baseline malnutrition was more likely for children living in Burkina Faso, with low birth-weight, never breastfed, and older age (12-24 months). Growth improved on ART, mainly within the first 6 months for weight, and was greater for the most severely malnourished children at baseline, but 8% to 32% remained malnourished after 24 months. Over the 24-month period of ART, there was a significant increase of hypercholesterolemia and decrease of anemia and hypoalbuminemia. CONCLUSIONS: Prevalence of malnutrition was high before ART initiation. Even though growth improved on ART, some children remained malnourished even after 2 years of ART, highlighting the need for more active nutritional support.Read less <