Objective To observe the treatment response and potential issues related to antiretroviral therapy (ART) in pediatric patients with acquired immunodeficiency syndrome (AIDS) and to provide a basis for revising the treatment guideline and improving the clinical practice. Methods Children eligible for ART according to the current treatment guideline were recruited from Dehong area. Enrolled patients were provided with ART and followed up for regular clinical check and laboratory tests. Results By the end of March 2009, a total of 70 children had received ART. Among them, 60 patients were treated with regimen including zidovudine (AZT)+ lamivudine (3TC)+nevirapine (NVP). Twelve, eighteen, twenty-three and nineteen patients have tested for HIV viral load after 3 month, 6 month, 12 month and 18 month treatment, respectively. Among them, 7, 12,14 and 14 patients respectively achieved HIV viral load lower than 1000 copy/mL. Average CD4+ Tlymphocyte count increased from (317.8±288.8) × 106/L at baseline to (1037.2±1086. 1) × 106/Lafter 18 month treatment. Side effects mainly occurred within the first 3 months of treatment. Nearly 50% of children had gastrointestinal symptoms. Resistance to 3TC, NVP and efavirenz (EFV) were found in five patients who have completed 12 months of treatment. Conclusions Pediatric AIDS patients show good compliance and treatment response to ART. Most side effects happen in the first 3months of treatment and the most common side effects are gastrointestinal symptoms.