Murine Lhx3 cDNA isolated from the mouse pituitary cDNA library encodes a LIM-type homeodomain protein that contains two tandemly repeated LIM domains and the homeodomain. The identities of predicted amino acid sequences between the mouse Lhx3 and Xenopus Xlim-3 genes are 80, 95, and 97% in the LIM domains 1 and 2, and the homeodomain, respectively, and 84% in the entire protein. 5′-RACE procedures and genomic cloning revealed that two distinct N-terminal sequences arise from two different exons 1a and 1b. Exon 1a encodes a sequence similar to that of Xlim-3, whereas exon 1b encodes a different N-terminus. It is likely that there are two transcription initiation sites in the Lhx3 gene. The Lhx3 transcripts were detected by whole mount in situ hybridization as early as day E9.5 post coitum in Rathke's pouch and the closing neural tube. During subsequent development, Lhx3 expression was observed in the anterior and intermediate but not in the posterior lobes of the pituitary, and in the ventral hindbrain and spinal cord. Northern blot analysis of adult tissues showed that Lhx3 mRNA persists in the pituitary. The expression pattern of Lhx3 is well conserved between Xenopus and mouse, underscoring the functional importance of this gene as a regulator of development. A number of established cell lines of pituitary origin express Lhx3 and therefore constitute a useful tool for further study of Lhx3 gene function. © 1995 Wiley-Liss, Inc.