Progression through meiotic development is in part controlled by an expression program that coordinates the timing of induction and time of function of numerous loci essential for the process. Whole-genome profiling of male germline expression in mouse, rat, and human provides important clues about the transcriptional regulatory machinery that drives the expression of its target genes. Among several thousand genes differentially expressed between testicular Sertoli and germ cells, a subset of conserved loci display highly similar meiotic and postmeiotic profiles across rodents and Homo sapiens. Mouse genes transcribed in the germline, but not in somatic control tissues, are frequently found to be important for sexual reproduction, thus correlating potentially specific expression and essential function in the male germline. In silico promoter analysis yields insight into DNA sequence conservation and the distribution of known regulatory elements within potential promoter regions of meiotic and postmeiotic genes. Some genes strongly expressed in male gonads are implicated in cancer, thus supporting the idea that gametogenesis and tumorigenesis may share molecular functions. Transcriptome, proteome, and protein network data reveal the kinetics of mRNA synthesis and translation in the germline, and help identify novel potentially important genes previously unassociated with the mammalian male germline.