Mammalian homologues of the Drosophila cut homeobox gene encode transcriptional repressors that are involved in tissue-specific and developmental gene regulation. We examined the expression of a murine cut homologue (Cux-1) in the adult mouse. In many somatic tissues, Cux-1 was expressed as a 13-kb transcript. However, the highest expression of Cux-1 was in the testis, where a unique 2.4-kb splice variant was identified. Less abundant transcripts of 5 kb, 6.5 kb, and 8.5 kb were also detected only in the testis. The nucleotide sequence of the 2.4-kb Cux-1 transcript was identical to the 13-kb transcript in the region of overlap, but the testis-specific transcript encoded a truncated protein that contained only one Cut repeat in addition to the Cut-related homeodomain. Studies of mice homozygous for the atrichosis (at/at) mutation suggested that the 2.4-kb transcript was expressed in germ cells in the testis. In situ hybridization verified that Cux-1 was transiently expressed in post-meiotic germ cells at the round spermatid stage. Immunoblot analysis of nuclear extracts showed that the testis-specific Cux-1 transcripts encoded a 55-kDa protein. These results demonstrate that multiple products of a cut-related homeobox gene are expressed in the testis. The highly restricted pattern of expression of Cux-1 in the testis suggests that it may be involved in regulation of postmeiotic gene expression.