Spermatogenesis is a complicated and poorly understood process that relies on the precise regulation of the self-renewal and differentiation of spermatogonia. In many organisms, microRNAs (miRNAs) are involved in multiple developmental processes as critical regulators of transcriptional and post-transcriptional gene silencing. This study investigated the expression pattern of miRNAs in type B spermatogonia cells (BSc) and primary spermatocytes (PSc) of mice, using a high-throughput small RNA sequencing system. The results revealed that the expression levels of Let-7 family miRNAs were remarkably high in both cell types. Furthermore, the expression levels of miR-21, miR-140-3p, miR-103, miR-30a, miR-101b and miR-99b were decreased during the transformation from BSc to PSc. These miRNAs target vital genes that participate in apoptosis, cell proliferation and differentiation, junction assembly and cell cycle regulation. These results highlight the indispensable role of miRNAs in spermatogenesis. Spermatogenesis is a complex process in which spermatogonial stem cells form spermatozoa following mitotic, meiotic and post-meiotic phases. The process of spermatogenesis is highly sensitive to fluctuations in the environment and involves numerous endocrine and paracrine signals to coordinate the self-renewal of spermatogonial stem cells (SCCs) and spermatogonial differentiation [1]. Spermatogenesis is characterized by the phase-specific expression of many genes that are exclusively expressed in spermatogenic cells.With the development and application of technologies such as gene cloning, gene expression and functional characterization, many spermatogenesis-related genes have been identified in the past few years, some of which were found to play important roles in spermatogenesis [2]. Spermatogenesis-associated genes such as cyclins, proto-oncogenes and genes for azoospermia factor, cytoskeleton, heat shock proteins, nucleoprotein transition, centrin and apoptosis are involved in highly conserved landmark events such as meiotic recombination, formation of the synaptonemal complex, sister chromatid cohesion, spermiogenesis during post-