Canine alpha3 and alpha4 chains of collagen type IV genes (COL4A3 and COL4A4) are expressed in the renal glomerular basement membrane, where they provide a critical structural and functional matrix for other basement membrane components. These genes are candidates for hereditary nephritis (Alport syndrome) in several dog breeds (e.g. English Cocker Spaniel and Bull Terrier). Using RACE and PCR, the cDNA of both genes was cloned and sequenced. Both COL4A3 and COL4A4, as well as canine NPPC (Natriuretic Peptide Precursor C), were mapped to CFA25 using an RH panel. Conservation of the tight linkage of COL4A3 and COL4A4 as seen in human and mouse was verified in the dog. Intron-exon boundaries in both genes were determined by BLAST analysis of the Canis Familiaris Trace Archive. The elucidation of the cDNA sequences, genomic organization and the open reading frames of canine COL4A3 and COL4A4 provide the groundwork for screening these genes for mutations in hereditary nephritis in dogs.