The accurate, spatially and temporally regulated gene expression is of fundamental importance for normal progress of spermatogenesis. Small non-coding RNAs that target gene expression at post-transcriptional and epigenetic level have turned out to be important players in gene regulation. Male germ cells express several classes of small RNAs, such as Dicer-dependent microRNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs), and Dicer-independent piwi-interacting RNAs (piRNAs). The goal of our research is to clarify the factors governing male fertility by investigating the functions of small non-coding RNAs and post-transcriptional gene control mechanisms during male germ cell differentiation. We have generated a knockout mouse model, which has Dicer1 gene specifically deleted in male germ cells. By using this model as a tool, we have elucidated the functions of Dicer-dependent small RNAs in spermatogenesis. piRNAs that are expressed predominantly in the germline, form a big, complex and functionally diverse group of small RNAs. piRNA expression is known to be greatly induced in late meiotic cells and round spermatids, and interestingly, we have demonstrated that in these cells, piRNAs accumulated in an intriguing cytoplasmic granule, a chromatoid body (CB). We have developed a CB isolation protocol to study the role of the CB in the piRNA-mediated functions and in the intra-cellular compartmentalization of RNA regulation. On the basis of our findings, the CB appears to be a central structure in haploid-specific RNA regulation. Most of the factors we are interested in are required for normal spermatogenesis in mouse, thus highlighting the importance of these pathways in male fertility.