X-Linked Alport syndrome is caused by mutations in the type IV collagen alpha5 chain gene. Male patients usually develop end-stage renal disease, whereas female patients have more variable phenotypes from asymptomatic hematuria to end-stage renal disease. The variable phenotypes in female patients may be attributable to different X-chromosome inactivation patterns. Therefore, the correlation between disease severity and the degree of alpha5 chain expression in the epidermal basement membrane of female patients with X-linked Alport syndrome was examined. To estimate the disease severity in X-linked Alport syndrome, the ratios of protein to creatinine in single voided urine samples were used. Expression of the alpha5 chain in the epidermal basement membrane was examined by an indirect immunofluorescence method using an anti-alpha5 chain monoclonal antibody. A total of 25 female patients with X-linked Alport syndrome from 17 families was examined. Multiple regression analysis using disease severity as the response variable, and age, family history of nephritis, female and male family history of end-stage renal disease, serum creatinine concentration, and alpha5(IV) expression ratio in the epidermal basement membrane as explanatory variables showed that only alpha5(IV) expression ratio was a significant factor, and that it showed a highly significant negative association with disease severity (adjusted r2=0.71, P=0.0001). These findings suggest that variable alpha5 chain expression, possibly caused by different X-inactivation patterns, is responsible for the variable disease severity in female patients with X-linked Alport syndrome, and that immunohistochemical examination of alpha5 chain expression in the epidermal basement membrane may be a simple and useful method for predicting patient outcome.