Aim of this study was to evaluate the presence of HIV-1 and CMV genomic sequences in myocardial tissue from autopsy of AIDS patients by in situ hybridization technique and to make a correlation with clinical and/or pathological signs of myocarditis. Seven patients out of 12 (58.3%) were positive for HIV-1 (6/7 patients with pathological signs of myocarditis and 1/5 without pathological abnormalities; p = 0.029). In situ hybridization for CMV was positive in 5/12 patients (41.7%) (3 with myocarditis and 2 without myocarditis); three clinically symptomatic cases were contemporary positive for HIV-1 and CMV. Our results seem to confirm emerging data about the presence of HIV-1 in myocardial tissue and about the possible role of HIV-1 in determining cardiac pathologies. Furthermore we suggest the hypothesis of an interaction of HIV-1 and CMV in latest of HIV infection.