Increased apoptosis in CD4+ T lymphocytes plays an important role in the pathogenesis of HIV infection and it has also invoked some HIV-related as well as antiretroviral-related adverse events. We assessed whether increased apoptosis is also present in the skeletal muscle of HIV-infected patients. We included 36 consecutive individuals, 18 without (group A) and 18 with HIV infection. The latter group consisted of five asymptomatic antiretroviral-naive HIV-infected individuals (group B), six asymptomatic HIV-infected individuals on highly active antiretroviral therapy (HAART, group C), and seven HIV-infected individuals on HAART with lipodystrophy (group D). Immunohistochemical reaction using deoxyribonucleotidyltransferase-mediated- dUTP-biotin nick-end labeling (TUNEL) was performed on skeletal muscle samples. None of the uninfected patients (group A) showed data of increased apoptosis, while 16 out of 18 infected patients did (p < 0.001). All subgroups of infected subjects (groups B-D) showed a significant increase of apoptosis in TUNEL with respect to uninfected individuals, but the comparison between the different subgroups of infected patients did not reveal significant differences. We conclude that skeletal muscle of HIV-infected patients exhibits increased apoptosis compared with that of uninfected patients, but the role of HAART in inducing apoptosis remains to be established.