To identify the abnormalities of the type IV collagen alpha 6 chain, alpha 6(IV), in Alport syndrome, we examined renal and skin tissue using rat monoclonal antibodies against non-consensus amino acid sequences of alpha 6(IV). Immunofluorescence of normal human kidney and skin tissue revealed linear alpha 6(IV) staining in the basement membrane (BM) of Bowman's capsule, in some tubules, and also in the epidermal BM. Renal specimens from five male patients of four families with X-linked Alport syndrome showed no reactivity for alpha 6(IV) in Bowman's capsules and tubules. In these patients, alpha 1(IV) and alpha 2(IV) were normal, whereas alpha 3(IV), alpha 4(IV), and alpha 5(IV) were absent from the BMs of the kidney. In skin tissue of male patients, neither alpha 5(IV) nor alpha 6(IV) were detected. The epidermal BM of female heterozygotes with X-linked Alport syndrome showed a mosaic staining for alpha 5(IV) and alpha 6(IV). These findings indicate that, in addition to a disturbed alpha 3(IV)-alpha 4(IV)-alpha 5(IV) network, patients with X-linked Alport syndrome have abnormalities in alpha 6(IV) of the renal and epidermal BMs at the protein level.