PURPOSE: To describe a macrodeletion spanning entire RCC1-like doman in the RPGR gene in one Japanese family with X-linked retinitis pigmentosa (XLRP). METHODS: Clinical ophthalmologic examinations were performed and genomic DNA was extracted from blood samples. Genomic DNA was analyzed by Southern blot and PCR amplification with specific primers. RESULTS: Patients had severe symptoms with early onset and rapid deterioration. PCR amplification and Southern blot analysis revealed the absence of the 5' half of the RPGR gene. The deletion was confirmed and characterized by designing flanking PCR primers: the deletion start point was located 80 bp upstream of the translation start site in exon 1, the end point was 42 bp downstream of exon 11. CONCLUSIONS: This 30 kb deletion contains the exons coding for the RCC1-like domain of RPGR. It is the first report of a macrodeletion that spans the entire RCC1-like domain of RPGR in X-linked retinitis pigmentosa patients, and suggests that loss of function of this domain disrupts the function of RPGR in human retina.