Spermatogonial stem cells (SSCs) are at the basis of the spermatogenic process and are essential for the continuous lifelong production of spermatozoa. Although several factors that govern SSC self-renewal and differentiation have been investigated, the direct effect of such factors on SSCs has not yet been studied, mainly because of the absence of markers to identify SSCs and the lack of effective methods to obtain and culture a pure population of SSCs. We now have used a previously established rat SSC cell line (GC-6spg) to elucidate the role of BMP4 in SSC differentiation. We found that GC-6spg cells cultured in the presence of BMP4 upregulate KIT expression, which is an early marker for differentiating spermatogonia. GC-6spg cells were found to express three BMP4 receptors and the downstream SMAD1/5/8 proteins were phosphorylated during BMP4-induced differentiation. A time-course DNA micro-array analysis revealed a total of 529 differentially regulated transcripts (≥2-fold), including several known downstream targets of BMP4 such as Id2 and Gata2. Pathway analysis revealed that the most affected pathways were those involved in adherens junctions, focal junctions, gap junctions, cell adhesion molecules, and regulation of actin cytoskeleton. Interestingly, among the genes belonging to the most strongly affected adhesion pathways was Cdh1 (known as E-cadherin), an adhesion molecule known to be expressed by a subpopulation of spermatogonia including SSCs. Overall, our results suggest that BMP4 induces early differentiation of SSCs in a direct manner by affecting cell adhesion pathways.