The aim of this study was to evaluate the influence of three variables--protease inhibitors, stavudine, and the length of combined therapy--on body habitus changes, metabolic effects and bone mineral density in HIV patients treated with highly active antiretroviral therapy (HAART). The onset of possible cardiovascular involvement was considered. Forty HIV patients (29 men and 11 women, mean age 39.13 +/- 7.82 years, range 28-61 years) treated with HAART for 12-43 months were evaluated for fat, lean, bone tissues, immunohematological and cardiovascular alterations. The differences in fat/lean tissues and bone mineral density were evaluated at dual-energy X-ray absorptiometry (DEXA). Serum lipids and the CD4/CD8 T-cell counts were recorded. ECGs were taken every 6 months; color Doppler echocardiography and color Doppler ultrasounds of the carotid vessels were performed in close chronological sequence with the second DEXA. Statistical analyses included: Student's t-test, Wilcoxon test, and single-multiple regression analysis. Thirteen patients presented with fat loss, 7 fat accumulation, and 20 a combined form of both. The changes in the single body districts showed that the decrease in the limb fat is to be attributed to protease inhibitors, while none of the three variables was responsible for the decrease in the upper limb fat. The trunk weight increase was not significant. The decrease in the lean mass of the upper limbs is to be attributed to protease inhibitors, while none of the three variables was responsible for the increase in the lean mass of the upper and lower limbs. The decrease in bone mineral density was not significant. No treatment-related cardiovascular lesions were observed. In HIV patients treated with HAART for 12-43 months, the decrease in lower limb fat was due to protease inhibitors. Neither osteopenia nor cardiovascular diseases were observed during follow-up.