Background: Two major Highly Active Antiretroviral Therapy naming as HAART-1(zidovudine, lamivudine and nevirapine) and HAART-2 (zidovudine, lamivudine and efavirenz) are considered for HIV positive patients. HIV as well as antiretroviral drugs can cause free radical formation with or without compensatory increase in serum selenium. This study was aimed at knowing serum levels of malonaldehyde (evidence of free radical production) and selenium. Method: A total of 240 persons were surveyed, comprising subjects and controls. The respondents were in four groups each comprising 60 persons. The four groups are: HIV positive patients not yet on HAART termed Prehaart patients, HIV positive patients on HAART-1, HIV positive patients on HAART-2 and HIV negative patients (control). Serum levels of malonaldehyde (MDA) and selenium were assayed in each of study groups. Result: CD4/mm 3 was significantly lower in subject groups when compared with control (p<0.05). MDA (µmol/l) was found to be higher in all subject groups but significant elevation was only found in HAART-2 group (p<0.05). Serum Se (µg/dl) levels were found to be significantly lower in all the groups when compared with control (p<0.05). Conclusion: Production of free radicals was worse in patients on HAART-2. Decreased serum selenium levels in all groups may suggest reason for oxidative stress found in HIV positive patients on antiretroviral therapy. Abbreviation: HAART-1(zidovudine, lamivudine and nevirapine), HAART-2(zidovudine, lamivudine and efavirenz), MDA (Malonaldehyde),Se (Selenium)