Canine X-linked hereditary nephritis is an animal model for human X-linked hereditary nephritis with a premature stop codon in the alpha 5(IV) gene of collagen type IV. We used this model to examine the other alpha(IV) chains at the mRNA and protein level in the kidney, since in human X-linked hereditary nephritis, the alpha 3(IV) and alpha 4(IV) chains are often absent from the glomerular basement membrane, although both are encoded by autosomal genes, cDNA probes for the alpha 1(IV)-alpha 6(IV) chains were generated from normal dog kidney using the polymerase chain reaction, Sequences were greater than or equal to 88% identical at the DNA level and greater than or equal to 92% identical at the protein level to the respective human alpha(IV) chains, By Northern analysis, transcripts for the alpha 1(IV), alpha 2(IV), and alpha 6(IV) chains were detected at comparable levels in both normal and affected male dog kidney RNA, As previously shown, the transcript for the alpha 5(IV) chain was reduced to similar to 10% of normal. Unexpectedly, the alpha 3(IV) and alpha 4(IV) transcripts were both decreased greater than or equal to 77% in affected male dog kidney, suggesting a mechanism coordinating the expression of these three basement membrane components, The NC1 domain of collagen type IV isolated from normal dog glomeruli was positive for the alpha 3(IV), alpha 4(IV), and alpha 5(IV) chains by Western blotting, In contrast, in the NC1 domain isolated from affected dog glomeruli, these three chains were not detectable, except for a trace of alpha 3(IV) dimer. In X-linked hereditary nephritis, the absence of the alpha 3(IV) and alpha 4(IV) chains from glomerular basement membrane may reflect factors acting at the transcriptional and/or translational level in addition to the protein assembly level.