Retinitis pigmentosa (RP) constitutes a major cause of blindness and the Retinitis Pigmentosa GTPase Regulator (RPGR) gene accounts for up to 80% of all X-linked RP cases. A novel isoform of RPGR, expressed in the human retina, was identified and characterized. It truncates the Regulator of Chromosome Condensation 1 (RCC1) homologous protein domain (RCC1h) of RPGR and mediates the formation of isoform-specific complexes with the RPGR-interacting protein 1 (RPGRIP1). Immunohistochemistry localized the novel RPGR isoform predominantly to inner segments of cone photoreceptors, where it colocalizes with RPGRIP1 in the human retina. In a patient with a mild RP phenotype, we identified a nucleotide substitution in a splicing regulator, which leads to 3.5 times higher levels of the transcripts coding for the novel RPGR isoform. The nucleotide substitution affects regulated alternative splicing of the novel RPGR isoform and suggests a tight adjustment of splicing as a prerequisite for proper function of photoreceptors.