Objective: Although the benefits of highly active antiretroviral therapy (HAART) have been documented, it is thought to be associated to disturbances in nutritional status. These disturbances may occur early in life and are poorly understood. The present study aimed to investigate the relationship between anthropometric parameters and body composition of perinatally HIV-infected children and adolescents under HAART, according to use and non-use of protease inhibitors. Design: Cross-sectional study undertaken between August and December 2007. Demographic, socio-economic, clinical and anthropometric data were collected from the patients. The χ 2 test, Wilcoxon rank sum test (Mann-Whitney) and t test were used to compare the following variables between users and non-users of protease inhibitors: age, gender, per capita income, HAART exposure, antiretroviral therapy adopted in the last three years, CD4 count, viral load, pubertal stage, nutritional status (BMI-for-age, height-for-age, waist and neck circumferences, triceps skinfold thickness, body fat percentage, upper-arm fat area and upper-arm muscle area). Setting: An HIV/AIDS out-patient clinic, São Paulo, Brazil. Subjects: One hundred and fifteen patients (children and adolescents aged 6-19 years). Results: Protease inhibitors users had a higher prevalence of stunting (P = 0·03), lower BMI (P = 0·03) and lower percentage of body fat (P = 0·05) compared with non-users. There was no statistically significant difference between the HAART regimens and measurements of fat adiposity. Conclusions: The findings of the study suggest that children and adolescents under protease inhibitors are at higher risk of growth and development deviations, but not at risk of body fat redistribution.