During meiosis, DNA replication is followed by two successive rounds of chromosome segregation (meiosis I and II), which give rise to genetically diverse haploid gametes. The prophase of the first meiotic division is highly regulated and alignment and synapsis of the homologous chromosomes during this stage are mediated by the synaptonemal complex. Incorrect assembly of the synaptonemal complex results in cell death, impaired meiotic recombination and aneuploidy. Oocytes with meiotic defects often survive the first meiotic prophase and give rise to aneuploid gametes. Similarly affected spermatocytes, on the other hand, almost always undergo apoptosis at a male-specific meiotic checkpoint, located specifically at epithelial stage IV during spermatogenesis. Many examples of this stage IV-specific arrest have been described for several genetic mouse models in which DNA repair or meiotic recombination are abrogated. Interestingly, in C. elegans, meiotic recombination and synapsis are monitored by two separate checkpoint pathways. Therefore we studied spermatogenesis in several knockout mice (Sycp1(-/-), Sycp3(-/-), Smc1beta(-/-) and Sycp3/Sycp1 and Sycp3/Smc1beta double-knockouts) that are specifically defective in meiotic pairing and synapsis. Like for recombination defects, we found that all these genotypes also specifically arrest at epithelial stage IV. It seems that the epithelial stage IV checkpoint eliminates spermatocytes that fail a certain quality check, being either synapsis or DNA damage related.