Our objective was to determine whether HIV-infected children treated with protease inhibitors (PIs) have different blood lipid, insulin, and glucose levels and body composition than HIV-infected children not treated with PIs. A cross-sectional cohort study was performed; in which 23 children were treated with combination antiretroviral therapy including a PI for at least 6 months and 12 children were treated with nucleoside reverse transcriptase inhibitors only (no-PI group). Levels of lipids, apolipoprotein B (apoB), insulin, and glucose were determined in the fasting state. Body composition and fat distribution were determined by anthropometric measurements and dual energy X-ray absorptiometry (DEXA) scan. Total cholesterol levels were higher in the PI-treated children (5.33 +/- 0.87 mM) than in the no-PI children (3.69 +/- 0.59 mM) (p < 0.0001). Similarly, low-density lipoprotein (LDL) levels were also elevated in the PI-treated children (3.27 +/- 0.76 vs. 2.14 +/- 0.51 mM) (p < 0.0001). ApoB and high-density lipoprotein (HDL), and to a lesser degree triglyceride levels, were also increased in the PI-treated children. Apart from percent arm fat as measured by DEXA, there were no differences between the two groups in measures of body composition or in their fasting glucose and insulin levels. The results from this cross-sectional cohort study suggest that the predominant lipid abnormalities associated with treatment with combination antiretroviral therapy including a PI in HIV-1-infected children are elevated total and LDL cholesterol.