A case of an adolescent male with renal-coloboma syndrome (RCS) showing developmental delay is described. Birth and perinatal histories were typical. Proteinuria was initially observed at the age of 7 years during an annual mass screening program for school children. His urine was checked periodically at a local hospital. Because of an increase in proteinuria, he was referred to our hospital for further clinical evaluation. Proteinuria was moderate, ranging from 1.0 to 1.5 g/day, and was coupled with mild renal dysfunction. At that time, he was found to have myopia associated with astigmatism. He exhibited mild developmental delay, assessed by a WISC-III test. A renal biopsy sample showed marked glomerular enlargement, collapse of glomerular capillaries, mesangial matrix expansion, and tubulointerstitial change, demonstrating typical histologic features of RCS. Approximately five years after starting follow-up, the patient had severe renal dysfunction. Furthermore, optic nerve coloboma was also evident. Genetic analysis of the patient revealed a novel heterozygous mutation in exon 3 of the PAX2 gene (P130H).