We have determined the genomic structure of the human LHX1 gene, a member of the LIM/homeobox (Lhx) gene family. The transcript is assembled from five exons, which are separated by introns ranging in size from 93 nt to 2.3 kb. The two LIM domains are entirely contained in the first and second exons, respectively, while the homeodomain is split into exons three and four. This structure closely parallels the organization of other mouse and human Lhx genes whose genomic structure is known. An exception is the mouse and human is/1 genes, whose homeodomain does not contain introns. An intron at the same position also occurs in the Xlim 1 gene as well as in other homeobox genes, such as evx1 and evx2, suggesting that this intron insertion represents an ancestral event, from which homeobox genes of different families originated. In this context, evolution of the Lhx gene family probably involved the shuffling of this intron-containing homeobox in the proximity of a LIM-only gene, while Islet genes were formed either by the shuffling of an intronless homeobox to the same LIM domain or, alternatively, by intron loss during their evolution.