Mouse knockout-models have previously revealed important biological functions of endothelin-converting enzyme-1 (ECE-1) in normal cardiac and craniofacial development. Since human ECE-1 is expressed in various isoforms, termed a, b, c, and d, expression of which is controlled by alternative promoters, we postulated that corresponding isoforms may also be transcribed from the murine Ece1 gene. By comparative sequence analysis using exon-specific sequences of human and rat ECE-1 we have resolved the complete exon-intron structure of the murine Ece1 locus on chromosome 4. The murine Ece1 gene comprises 23 exons distributed over 100 kb of genomic DNA and was found to be structurally highly conserved when compared to the human ECE1 gene. As with the human gene, the exons containing isoform-specific sequences were localised in the 5' terminal region of the murine Ece1 gene. Using specific sense primers, isoform-specific expression of murine ECE-1 mRNA in various mouse tissues was confirmed by RT-PCR. Using real-time PCR we demonstrated that ECE-1c was the most abundantly expressed isoform in most tissues, except for heart and aorta displaying a more even isoform distribution. We detected an additional isoform-specific exon, designated c2, which was apparently constitutively spliced and expressed only as minor fraction of ECE-1c transcripts. Our results provide evidence of structural conservation of mammalian genes encoding ECE-1 and will facilitate a more refined analysis of ECE-1 mRNA expression in the mouse model organism.