Deleted in Azoospermia Associated Protein 1 (DAZAP1) is a ubiquitous heterogeneous nuclear ribonucleoprotein (hnRNP) that is expressed abundantly in the testis. DAZAP1 deficiency in mice results in growth retardation and spermatogenic arrest. Previous reports on DAZAP1's binding to several naturally occurring splicing mutations support a role for DAZAP1 in RNA splicing. To elucidate the biological function(s) of DAZAP1 and to search for its natural RNA substrates, we used microarrays to compare the expression profiles and exon usages of wild-type and Dazap1 mutant testes and identified three genes (Crem, Crisp2 and Pot1a) with aberrant RNA splicing in the mutant testes. We further demonstrated that DAZAP1, but not DAZAP1 mutant proteins, promoted the inclusion of Crem exon 4, Crisp2 exon 9 and Pot1a exon 4 in splicing reporter transcripts in cultured cells. Additional studies on the binding of DAZAP1 to the exons and their flanking intronic sequences and the effects of minigene deletions on exon inclusion identified regulatory regions in Crem intron 3, Crisp2 intron 9 and Pot1a intron 4 where DAZAP1 bound and regulated splicing. Aberrant splicing of the Pot1a gene, which encodes an essential protein that protects telomere integrity, may partially account for the growth retardation phenotype of DAZAP1-deficient mice.