Germ cells are unique in their capability to give rise to a new organism. In addition to genetic information, the epigenetic status of cells is inherited, which emphasizes the importance of securing both genetic integrity and correct epigenetic marks in the germline. The alarming decline in the semen quality and reproductive health in Western countries has unveiled the necessity of understanding the genetic, epigenetic and environmental factors governing male reproductive functions. Male germ cell differentiation is orchestrated by accurate, spatially and temporally controlled gene expression patterns. Male germ cells express outstanding amount of different non-coding RNAs, including both small RNAs and yet poorly characterized long non-coding RNAs. Small non-coding RNAs are important regulators of gene expression that mainly function at the post-transcriptional level. Small RNAs produced by the male germline include 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 roles of non-coding RNAs and the mechanisms of post-transcriptional gene control during male germ cell differentiation. We have shown that Dicer-dependent pathways are required for normal spermatogenesis and male fertility by analyzing a knockout mouse model to delete Dicer1 gene specifically in early postnatal male germ cells. Our results demonstrate that Dicer is crucial for the correct nuclear polarization and chromatin condensation of developing spermatids. 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 shown that in these cells, piRNAs accumulate in an intriguing male germ cell -specific cytoplasmic ribonucleoprotein granule, a chromatoid body (CB). We have isolated CBs from mouse testis and identified its molecular composition by mass spectrometric analysis and RNA sequencing to better understand its functions in haploid cells. The CB appears to act as a central RNA regulation platform as it accumulates a multitude of different RNA-binding and RNA-processing proteins as well as several RNA species including piRNAs, mRNAs and long non-coding RNAs. All the results indicate that the CB has an important role in the regulation of meiotic and post-meiotic processes. Many of the CB components are essential for normal spermatogenesis in mouse, which highlights the significance of this structure in maintaining male fertility.