A 5-kb long transcript encoding the stearoyl-CoA desaturase (SCD) was identified by Northern-blot analysis of poly(A)+ mRNA from caprine lactating mammary gland. Complete sequencing of the SCD cDNA (5123 bp) revealed that the coding region (1080 nt) is followed by an unusually long (3.8 kb) 3'-UTR sequence, deriving from a single exon, in which a polymorphism, due to the deletion of a nucleotide triplet, was detected. The complete structural organization of the relevant gene has been determined. The transcription unit was shown to span a 15-kb region and to consist in six exons varying in size from 131 (3rd exon) to 4047 bp (6th exon), and five introns varying in size from 600 to 3700 bp. Using the fluorescence in situ hybridization technique, the SCD gene was localized to bovine and caprine chromosomes 26q21, and ovine chromosome 22q21.