ID3 is a transcription factor that acts as a dominant-negative regulator of other transcription factors by sequestering them, thus rendering them unable to bind DNA. We have shown previously that ID3 is expressed in a unique, region-specific manner along the epididymis, a highly specialized tissue of the male reproductive tract that functions in the transport and maturation of spermatozoa. The goal of these studies was to test the hypothesis that ID3 plays a role in the epididymis in the region-specific regulation of gene expression that is responsible for establishing the microenvironment required to carry out sperm-related functions. The consequences of ID3 deficiency on epididymal histology and gene expression profiles, as well as spermatozoal motility parameters, were determined. Although ID3 deficiency (Id3^−/− mice) had no noticeable impact on epididymal histology, the targeted mutation adversely affected sperm motility parameters. Moreover, principal component analysis of microarray data indicated that the gene expression signatures for tissues obtained from Id3^−/− mice and their genotypic controls were distinct from each other in each epididymal region. The predominant effect of the Id3 null mutation was in the cauda region where the expression of many transcription factors, including Hoxb8 and Bclaf1, was markedly affected. ID3 may play an important role in the molecular circuitry involved in the establishment and maintenance of the region-specific differences in gene expression that are characteristic of the epididymis.