Homeobox genes have been demonstrated to play important roles during cancer differentiation and embryonic development. The subset of Iroquois-related homeobox genes (IRXs) have furthermore been demonstrated to be involved in several embryonic developmental processes such as patterning of the anterior-posterior and dorso-ventral axis, as well as specific regions of the central nervous system, and differentiation of the otic vesicle, branchial epithelium, and limbs. We have characterized a novel homeodomain protein and corresponding gene by means of computational biology. Since the protein sequence displayed high similarity to the human IRX proteins, the newly identified homeodomain protein was named Iroquois family related homeodomain protein (IFRX). The IFRX protein sequence was found to be highly conserved in vertebrates. The corresponding IFRX gene was located on chromosome 10p12.1 and is organized in seven exons. The protein is predicted to be localized to the nucleus, supporting evidence for a functional role as a transcription factor, as suggested by the existence of a homeodomain. Preliminary expression profiling by biocomputational means predicted a rather broad expression profile with expression in the bone marrow, brain, heart, kidney, liver, lung, pancreas, prostate, skeletal muscle, spinal cord, spleen and thymus. However, expression in several tissues seemed to be low. In addition, approximately one third of all available EST sequences were obtained from embryonic tissues, suggesting that IFRX has a role in embryonic development.