Type I Bartter syndrome (BS) is caused by mutations of the Na-K-2Cl cotransporter (NKCC2)-encoding SLC12A1 gene. The clinical phenotype of this severe form of BS is characterized by polyhydramnios, premature delivery, failure to thrive, and nephrocalcinosis, and the diagnosis is usually made during the antenatal-neonatal period. This report concerns a 29-year-old Japanese man with atypical type I BS due to a compound heterozygous mutation of the SLC12A1 gene. He was born after full-term pregnancy complicated by polyhydramnios. He first presented with asymptomatic proteinuria at the age of 20 years and was diagnosed with BS based on laboratory data. There were signs of moderate proteinuria, mild renal dysfunction and nephrocalcinosis. Renal biopsy showed focal segmental glomerulosclerosis (FSGS), and genetic testing revealed novel mutations of A555V and G809V in the SLC12A1 gene. The patient's sister showed the same clinical course, laboratory test abnormalities and gene mutations. Our patient had a type I BS with an atypical clinical course, which was diagnosed when he was 20 years old. Laboratory findings indicated phenotypic variability in this disease, and the presence of nephropathy suggested that FSGS might be one of the lesions causing end-stage renal failure in this disease.