During spermatogenesis, diploid stem cells differentiate, undergo meiosis and spermiogenesis, and transform into haploid spermatozoa. Various factors have been demonstrated to regulate this marvelous process of differentiation, but the expression of only a few genes specifically involved in spermatogenesis has been studied. In the present study, different types of spermatogenic cells were isolated from Balb/c mice testes of different ages using the velocity sedimentation method, and we determined the expression profiles of 1176 known mouse genes in six different types of mouse spermatogenic cells (primitive type A spermatogonia, type B spermatogonia, preleptotene spermatocytes, pachytene spermatocytes, round spermatids, and elongating spermatids) using Atlas cDNA arrays. Of the 1176 genes on the Atlas Mouse 1.2 cDNA Expression Arrays, we detected 181 genes in primitive type A spermatogonia, 256 in type B spermatogonia, 221 in preleptotene spermatocytes, 160 in pachytene spermatocytes, 141 in round spermatids, and 126 in elongating spermatids. A number of genes were detected as differential expression (up-regulation or down-regulation). Fourteen of the differentially expressed genes have been further confirmed by reverse transcription-polymerase chain reaction for their expression characterizations in different types of spermatogenic cells. These results provide more information for further studies into spermatogenesis-related genes and may lead to the identification of genes with potential relevance to spermatogenesis.