The testes of AIDS patients invariably show decreased spermatogenesis and are atrophic. These testicular changes can be grouped into three categories: (1) spermatogenesis present, but decreased; (2) spermatogenic arrest at primary spermatocyte stage; and (3) Sertoli only (or almost Sertoli only). The purpose of this study is 2-fold: firstly, to quantitate the numbers and types of germ cells in these three groups as compared with normals. In addition the presence of HIV-1 DNA positive germ cells was quantitated by PCR in situ hybridization. HIV-1 was identified in 14 of 15 testes from HIV infected adults, and was present in 25-33% of residual germ cells. There was an average of 18.9 HIV infected germs cells/tubule in the spermatogenesis group, 6.3 HIV infected germs cells in the spermatogenic arrest group, and 0.25 HIV infected germ cells in the almost Sertoli only group. HIV-1 DNA was absent in three of the three preadolescent boys testes (HIV acquired in utero). This study quantitates the degree of germ cell loss in AIDS patients and quantitates the degree of HIV positivity of the residual germ cells, thus shedding more light on the testicular HIV burden, with its possible repercussions for sexual transmission of HIV.