The sequence and genomic organization of the mouse Lim1 gene were determined. The mouse Lim1 gene has five coding exons. The Lim1 transcription initiation start site was determined by 5' RACE. indicating that the first exon encodes the translation initiation codon and a 1360-bp 5' untranslated region. Sequence analysis of the 450-bp upstream of the transcription start site revealed the presence of a CATTAA motif at -32 bp and a CAATT box located in reverse orientation at -68 bp. HNF3 beta and Pbx1 binding sites were also identified. Like most LIM domain encoding genes, the LIM domains of Lim1 are each encoded on separate and adjacent exons. Knowledge of the sequence and structure of the mouse Lim1 gene provides important information for the genetic manipulation of the Lim1 locus.