Comparisons of body composition and metabolic changes among antiretroviral-naive patients randomly assigned to didanosine and stavudine- (ddI + d4T) vs. abacavir and lamivudine- (ABC + 3TC) containing regimens were assessed in a nested substudy of an ongoing multicenter randomized trial. At baseline and every 4 months, body cell mass and total body fat were calculated, anthropometric measurements were performed, and fasting metabolic parameters were obtained. The rates of change (unit/mo) estimated using the slopes of regression lines and overall mean changes from baseline were compared by study assignment. Among 96 patients enrolled, 46 received ddI + d4T- and 50 received ABC + 3TC-containing regimens with a median follow-up of 32.4 months. For both study arms, an overall increase in the rates of change was seen for body cell mass. For ddI + d4T, after an initial increase, the rates of change declined for regional fat and total body fat compared with an increase for ABC + 3TC, with the 2 arms being significantly different (P < 0.05). For high-density lipoprotein cholesterol rates of change, ddI + d4T decreased, while ABC + 3TC increased. For both arms, low-density lipoprotein cholesterol decreased, while triglycerides increased. Early and sustained increases in insulin and insulin resistance were seen only for ddI + d4T. In this prospective study, metabolic and body composition changes varied according to whether subjects received ddI + d4T or ABC + 3TC.