We have previously cloned the murine Lhx3 cDNA that encodes a predicted protein containing two tandemly repeated LIM domains and a homeodomain. Early expression of Lhx3 in oral ectoderm that is committed to contribute to the anterior and intermediate lobes of the pituitary and its perseverance in the adult gland strongly suggest an involvement of the gene in mediating and maintaining the differentiation program of this important endocrine system. Additional functions are suggested by the fact that Lhx3 is also expressed bilaterally along the spinal cord and the hindbrain at early stages of mouse development. Here we report the structural organization and chromosomal localization of the Lhx3 gene. The gene is composed of six exons and five introns. Two different exons, Ia and Ib, appear to be alternatively spliced to exon II. The first LIM domain is encoded by exon II and the second by exon III. The homeobox is shared by exons IV and V. We have mapped Lhx3 to the proximal region of mouse chromosome 2 in a region that shares homology with human chromosomes 9q and 10p.