<span class="paragraphSection"><div class="boxTitle">Abstract</div>Minor intron-containing genes (MIGs), which require the minor spliceosome (MiS) for their splicing, are highly represented among genes involved in mouse spermatogenesis. Leveraging gene- and intron-level ortholog data, we show that conservation of these genes as MIGs is particularly strong in chordates but not in other species groups, suggesting lineage-specific changes to their splicing regulation. A role for the MiS in splicing during spermatogenesis was reinforced by the cell-type specific expression patterns of MiS small nuclear RNAs (snRNAs) and directly tested using Stra8-Cre mediated ablation of <span style="font-style: italic;">Rnu11</span>, which encodes for the MiS U11 snRNA. <span style="font-style: italic;">Rnu11</span> mutant testes were smaller, and presented with multiple mitotic and meiotic defects, increased cell death, and a reduction in mature sperm at matched timepoints. RNA sequencing of P14 whole testes revealed minor intron retention and alternative splicing events in MIGs that are key regulators of genomic stability, cell cycle progression, and gene expression regulation, contributing to the variable cellular defects. RT-PCR of fractionated cell types of the testes confirmed splicing defects of key MIGs in cell-type enriched samples. The multifaceted molecular disruption resulted in defective meiotic recombination, telomere morphology, chromosome synapsis, and XY-chromosome association. Overall, we highlight the molecular and cellular processes that are regulated by the MiS.</span>