The mouse Hox gene family is a set of mammalian homeobox genes that may represent developmental control genes. Complete information about the primary structure of these genes is a prerequisite for a systematic analysis of the mechanisms that determine their complex tempero-spatial expression patterns. In this report we describe the complete sequence of the Hox-3.1 locus and provide evidence for several closely spaced transcriptional start sites. Sequence analysis of the 5' region of the Hox-3.1 gene extending to its nearest upstream neighbor, Hox-3.2, allowed us to identify sequences known to be capable of interactions with transcription factors. Several of these sequence motifs are similar to cis-regulatory elements found in the regulatory regions of other known developmentally regulated genes.