The BS69 protein has been commonly described as a co-repressor associated with various transcription factors. However, this hypothesis relied predominantly on overexpression of tagged proteins due to the lack of a reliable BS69 antibody. We present for the first time a complete sequence of BS69 and valuable tools to characterize the endogenous protein. We show that the full-length BS69 protein, as well as minor alternatively spliced isoforms, is ubiquitously expressed, nuclear, and associates with chromatin and mitotic chromosomes. Accordingly, BS69 interacts with a set of chromatin remodeling factors, including ATP-dependent helicases, histone deacetylases, and histone methyltransferases, as well as the E2F6 transcription factor. These data strengthen a role for BS69 in gene repression and link BS69 to chromatin remodeling.