The course of renal involvement and hearing loss is much milder in most female X-linked Alport syndromes than in male patients. We examined the molecular mechanism of development of the disease in a female patient with severe Alport syndrome. The patient showed heavy proteinuria, hematuria, neurosensory hearing loss and primary amenorrhea. Renal biopsy findings of electron microscopy and immunostaining of the alpha5 chain of type IV collagen indicated a female X-linked Alport syndrome. G-banding chromosomal analysis showed a t(X;1)(q22.3;p36.32) balanced translocation. Analysis of the collagen type IV (COL4A5) gene by genomic DNA sequencing, complementary DNA (cDNA) sequencing and multiplex ligation-dependent probe amplification assay showed no mutations or deletions/duplications of the gene. However, fluorescence in situ hybridization using the probes for exon 1 and exon 51 of the COL4A5 gene showed disruption of one copy of the gene. Replication R-banding chromosomal analysis indicated preferential inactivation of the normal X chromosome. This is the first report of severe Alport syndrome in a female patient carrying a balanced translocation between the chromosome X and 1 producing the disruption of one copy of COL4A5 gene and silencing of the other copy because of preferential inactivation of the normal X chromosome. Chromosomal abnormalities should be considered in female patients with severe forms of Alport syndrome.