Histone deacetylases (HDACs) play a central role in the modification of chromatin structure and thus in the regulation of transcription and cellular differentiation. Based on structural and functional similarities, mammalian histone deacetylases may be grouped into four categories: class I HDACs, which are homologs of the yeast histone deacetylase RPD3; class II HDACs, which share a significant degree of homology with the yeast histone deacetylase HDA1; class III HDACs, which are closely related to the yeast SIR2 protein; and the most recently described class IV of HDACs, which comprises HDAC11-related enzymes. We have isolated and characterized the human HDAC11 genomic sequence, which spans a region of 24,074 bp and has a single genomic locus. Determination of the exon-intron splice junctions established that HDAC11 is encoded by 9 exons ranging in size from 43 bp (exon 4) to 867 bp (exon 9). Characterization of the 5' flanking genomic region, which precedes the HDAC11 open reading frame, revealed a TATA and CCAAT box-less promoter that contains a 1-kb CpG island. The 1,733-bp human HDAC11 mRNA encodes a 347 aa protein with a predictive molecular weight of 39.1 kDa and an isoelectric point of 6.88. Fluorescence in situ hybridization analysis localized the human HDAC11 gene to chromosome 3p25, a region characterized by frequent gains and losses of chromosomal material in a number of various types of cancer.