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Spermatocytes undergo meiosis to give rise to round spermatids, which in turn metamorphose to flagellated spermatozoa that mature in the epididymis. To characterize the dynamics of gene expression during these important stages of spermatogenesis, we undertook transcriptome analysis in &gt;90% pure pachytene spermatocytes and round spermatids, and pure mature sperm of rat by massive parallel deep sequencing. The study has identified 10,719 total transcripts expressed in meiotic and postmeiotic cells, out of which 7,641 were present in all the three cell types. Most abundant transcripts were related to gametogenesis in spermatocytes and spermatids, and mitochondrial energy metabolism in sperm. Importantly, 108 transcripts were specific to spermatocytes, including <jats:italic>Cpeb2<\/jats:italic>, <jats:italic>Dpf3<\/jats:italic>, <jats:italic>H2afy<\/jats:italic>, <jats:italic>Haus7<\/jats:italic>, <jats:italic>Plcb1<\/jats:italic>, <jats:italic>Taf9<\/jats:italic>, and <jats:italic>Tdrd7<\/jats:italic> strongly linked with meiosis. Similarly, 323 transcripts unique to round spermatids included <jats:italic>Arpc5<\/jats:italic>, <jats:italic>Apoa1<\/jats:italic>, <jats:italic>Cntrob<\/jats:italic>, <jats:italic>Dcaf17<\/jats:italic>, <jats:italic>Ift88<\/jats:italic>, and <jats:italic>Ly6k<\/jats:italic> that play essential roles in spermiogenesis. Likewise, 178 transcripts unique to sperm included <jats:italic>Camta1<\/jats:italic>, <jats:italic>Hoxb1<\/jats:italic>, and <jats:italic>Prdx6<\/jats:italic> having assigned roles in fertility and\/or embryonic development. Levels of ~16% transcripts declined from spermatocytes to sperm while two (<jats:italic>Cd300e<\/jats:italic> and <jats:italic>Ddx17<\/jats:italic>) increased. New candidate genes with possible roles in meiosis (91), spermiogenesis (298), and sperm function (171), have been identified. This study has provided new potential targets for contraception and\/or treatment of male infertility. 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