Divergent homeobox genes function as transcription factors and have been shown to be important in mammalian development. Hex is a divergent homeobox gene that we have previously reported to be expressed in E12.5 mouse lung, thyroid and liver. To gain insight into the function of Hex, we completed an extensive analysis of Hex expression by in situ hybridzation, northern analysis and RT-PCR. We also isolated genomic DNA for Hex for use in identifying its chromosomal localization and for gene targeting experiments. Hex is first expressed at E7.0 in the mouse during gastrulation. At this age, Hex expression is limited to cells at the distal end of the egg cylinder which constitute the primitive endoderm. This region includes the future gut endoderm, the notochord and/or the node. At E9.5, Hex is highly expressed in the hepatic primordium and in the rostral region of the foregut that is to become the thryoid gland. At E10.5, strong expression is seen in the liver, gall bladder, pancreas, thyroid diverticulum and in the branchial arch region. Lung expression, which first appears at E11.5 - 12, appears to involve both the mesenchyme and epithelium of the distal lung. At E12 - 13.5, high levels of expression continue in the thyroid, liver and pancreas with lower levels detected in the lung and thymus. At E16.5, Hex RNA can be still be detected in the thyroid, thymus, lung, liver and pancreas but at lower levels than at E13.5. At this age, levels of expression are highest in the thyroid and are comparable in all other domains. In adult mice, expression of Hex persists in the thyroid, thymus, liver, and lung and may be increased in the liver above levels seen at E16.5. Additionally, we detected Hex expression in mature mouse thymic stromal cells; adult rat hepatocytes and cholangiocytes; and the rat thyroid epithelial cell line FRTL-5. Using FISH analysis, we localized the Hex gene to the distal end of mouse chromosome 19, which is syntenic with human 10q.19 - 10q.26. The restricted expression of this divergent homeobox gene suggests that it may play an important role during gastrulation or early endoderm specification, during organ development in mid-gestation mice, as well as a separate organ specific role in mature animals.