The vast majority of cases of spermatogenic failure, defined as no sperm in semen or low semen quality, are idiopathic, although several genetic factors have been identified. In this thesis, we focused on the effect of Y-chromosome variation including TSPY copy number and AZFc deletions on semen quality and studied the effectiveness and safety of in vitro spermatogonial stem cell propagation for (SSC) transplantation as a potential treatment for spermatogenic failure by increasing the number of SSCs. We found that the variation in TSPY copy number is not associated with total motile sperm count and therefore has no functional consequences for semen quality. AZFc deletions are known to be common genetic causes of spermatogenic failure. We showed that in our previously established culture system, the AZFc-deleted spermatogonia behave similar as spermatogonia from non-deleted men. To further characterize the human SSCs in our culture, we investigated which marker is efficient in enriching for SSCs. We found that ITGA6 (using magnetic assisted cell sorting or MACS) is an efficient method for enrichment of SSCs. We then investigated the genetic and epigenetic stability of human SSCs after long-term culture and showed that genetic stability of SSCs is preserved during culture. However, the methylation status of some of the imprinted genes is changed, which requires further investigation. We concluded that in vitro propagation of human SSCs followed by transplantation could be a good potential treatment option in patients with a low number of functional SSCs due to genetically caused spermatogenic failure.