BACKGROUND It is estimated that about 2.5 million people are living with HIV infection in India. Although antiretroviral drugs have been able to reduce the mortality, these drugs have serious side effects one of which is lipodystrophy syndrome. Most of the drugs used in HAART viz, protease inhibitors, stavudine and nevirapine are associated with lipodystrophy. Hence we conducted this study to assess the prevalence of lipodystrophy in HIV infected children on HAART and its associated risk factors. METHODS A cross sectional study was conducted on 80 HIV infected children aged 2-18 years of age who were on stavudine based HAART for ≥ 2 years. These children were assessed for presence of lipodystrophy, its metabolic complications and associated risk factors. RESULTS Lipodystrophy was observed in 33.7% of children with lipoatrophy being the commonest subtype followed by lipohypertrophy. Older age, increased duration of treatment and dyslipidaemia were found to be associated in patients with lipodystrophy than those without. On further multivariate analysis of independent risk factors only increased duration of treatment was significantly associated with lipodystrophy. No association was found with insulin resistance. CONCLUSIONS We observed that lipodystrophy is a common finding in HIV patients treated with HAART for long duration.