Alport syndrome (AS) is a progressive hereditary glomerulonephritis presented with hematuria, progressive renal failure, sensorineural deafness, and ocular lesions. Females with X-linked Alport syndrome (XLAS) have variable phenotypes, from asymptomatic hematuria to renal failure. In order to understand the possible mechanism of different phenotypes in female XLAS, we analyzed mRNA expression level of the mutant COL4A5 gene in fibroblasts, the X-inactivation pattern in peripheral blood DNA, and the phenotype variability of XLAS females. Total RNA was isolated from cultured skin fibroblasts in five females with XLAS and confirmed deletion mutations of COL4A5 mRNA. Reverse transcription-polymerase chain reaction (PCR) was performed to amplify the fragment, including the mutation sequences of the COL4A5 gene. The PCR products were electrophoresed with 8% polyacrylamide gel. Messenger RNA expression level of the mutant COL4A5 gene was analyzed with the optical density of PCR product revealed under polyacrylamide gel. The X-inactivation analysis was performed using HpaII predigestion of peripheral blood DNA followed by PCR of the highly polymorphic CAG repeat of the androgen receptor (AR) gene. All patients in the study had persistent microscopic hematuria. Two of them had gross hematuria. Three cases had persistent and severe proteinuria of 2+~3+, and the others had discontinuous and milder proteinuria of - ~+. The patients whose mRNA expression level of the mutant COL4A5 gene was higher had persistent and more severe proteinuria (r = 0.975, P = 0.005). None of them had skewed X inactivation. Our preliminary results demonstrate that the quantity of mRNA expression level of the mutant COL4A5 gene was correlated with the phenotypic severity of females with XLAS, and this could not be explained by X-inactivation pattern in peripheral blood leukocytes.