BackgroundWith the advent of highly active antiretroviral therapy (HAART), HIV infection has become a chronic condition in children with improved survival and quality of life. Reports on long term effectiveness of non-nucleoside reverse transcriptase inhibitor based HAART in HIV-infected children in developing countries are limited.MethodsA chart review was conducted and children who received at least six months of HAART between 2004–2011 at All India Institute of Medical Sciences (AIIMS), Delhi were included. The clinical, immunological and virological responses to HAART were documented. Factors predicting non-adherence and non-response to treatment were described.ResultsOne seventy five children (boys: 74.9%) were included in the study, with a median follow up of 43 (IQR:17, 68) months. The median age at diagnosis was 119 (IQR: 75, 156) months. The median CD4 count at start of HAART was 340 cells/μL (IQR: 185,704), which increased to 924 cells/μL (IQR:591,1278) at 48 months after HAART and plateaued at 749 (IQR: 542,1056) cells/ μL after 90 months of therapy. The weight for age (WAZ) and height for age (HAZ) z score both showed improvement with time after HAART initiation [baseline: WAZ −2.8 (IQR:-4,-1.6), HAZ −2.1 (IQR:-3.4,-0.69); at 42 months of therapy: WAZ −1.2 (IQR:-2.1, 0.01), HAZ −0.75(IQR:-1.6,-0.37)]. Adverse events were reported in 21 (12%) children. Non-adherence to therapy, treatment failure and death were noted in 35 (20%), 9 (5.1%) and 6 (3.4%) children respectively.ConclusionsOur experience shows that HAART in HIV-infected children is effective, safe and is associated with good immunological and virological response as well as improvement in growth parameters.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-014-0701-2) contains supplementary material, which is available to authorized users.