Covalent modification of histones regulates chromatin structure and gene expression. Sin3A mediates the association of histone deacetylase enzymes with a large number of sequence-specific transcriptional repressors. In this study we characterized three novel transcripts of SAP30L, a recently identified Sin3A-associated protein. These splice variants show significant differences in transcriptional repression capabilities and associating histone deacetylase activities. Furthermore, they differ in binding to Sin3A and in subcellular localization when transiently transfected. These data suggest that the transcriptional repression of a Sin3A corepressor complex can be regulated not only by sequence-specific transcriptional repressors, but also by modification of associated proteins, such as SAP30L.