Corepressor BS69 interacts with ZHX1, a member of the ZHX family having zinc-fingers and homeoboxes. In the rat, we have identified four forms of splicing variants, BS69alpha, BS69beta, BS69gamma, and BS69delta. Based on the amino acid sequence, BS69alpha corresponded to the human orthologue. BS69beta and BS69gamma contain a novel 56 amino acid region encoded by the exon 11b of the rat BS69 gene. Both BS69gamma and BS69delta lacked a region encoded by exon 3 of the gene. Although all four variants were ubiquitously expressed in rats, the transcripts having the exon 11b were detected in mice and rats but not in humans. A common C-terminal MYND domain of BS69 was required for the interaction with PxLxP motif of ZHX1. Although BS69 was originally found as a corepressor interacting with ZHX1, BS69 was also found to function as a transcriptional activator in HEK293 cells, in which the activation required the MYND domain of BS69. Co-transfection of BS69 with a mutant form of ZHX1, which cannot interact with BS69, led to increase the transcriptional activation of BS69, suggesting that transcriptional activation mediated by BS69 is suppressed by ZHX1. In contrast, BS69 showed transcriptional repression in COS-7 and CV-1 cells and the repression domain was mapped to the N-terminus of BS69beta. Both the wild type and mutant form of ZHX1 had no effect on the BS69 repression, suggesting that the repression mediated by BS69 in COS-7 and CV-1 cells may require a cofactor other than ZHX1 in the cells. Therefore, our results suggest that BS69 may function either as a transcriptional repressor or as a transcriptional activator depending on its regulatory partner.