A key step in the investigation of male infertility is the appropriate classification of impaired spermatogenesis. In this study, we precisely identified Sertoli and distinct germ-cell types in the rat, the mouse, and in the human testis. As a proof of principle, we studied testis biopsy samples from azoospermic patients with defined spermatogenic defects. Remarkably, we found that already the numbers of Sertoli cells, spermatogonia and a subset of spermatogonia including stem cells are significantly reduced in patients with maturation arrest at the level of primary spermatocytes (n=33) compared with patients with histologically normal spermatogenesis (n=33). In patients with hypospermatogenesis (n=44) a significant reduction of spermatogonial cell numbers was observed. The numbers of primary and diplotene spermatocytes were reduced by 84%. However, the strongest reduction (96%) was revealed in the numbers of spermatids in patients with maturation arrest. In contrast, patients with hypospermatogenesis showed only modestly reduced numbers of spermatocytes and spermatids compared with normal spermatogenesis. No correlation was found with age or obstruction. For a detailed analysis of the patients, we distinguished between 'pool of founder cells'-related deficiencies (reduced numbers of Sertoli cells, spermatogonia, and spermatogonial stem cells) and 'meiotic' deficiencies (reduced numbers of spermatocytes, meiotic divisions, and spermatids). Interestingly, patients with maturation arrest showed meiotic deficiencies (36%), while the majority additionally demonstrated deficiencies in the founder pool (58%). In contrast, patients with normal spermatogenesis most often had no deficiencies at all (45%) or founder pool-related deficiencies (33%) but an apparently normal meiosis. This is the first report showing that many infertile patients face besides meiotic defects the problem of reduced numbers of Sertoli cells, spermatogonia, and spermatogonial stem cells.