X-linked ocular albinism type 1 (OA1) is caused by mutations in G protein-coupled receptor 143 (GPR143) gene, which encodes a membrane glycoprotein localized to melanosomes. GPR143 mainly affects pigment production in the eye, resulting in optic changes associated with albinism, including hypopigmentation of the retina, nystagmus, strabismus, foveal hypoplasia, abnormal crossing of the optic fibers, and reduced visual acuity. We report the mutational analysis of the GPR143 gene on two unrelated families with OA1 using direct sequencing and real-time quantitative polymerase chain reaction. We identified the c.564_565delCT, a 2-bp deletion in family 1, and we mapped the breakpoints at nucleotide level of the novel intragenic deletion g.5360_6371del1012, encompassing exon 2, in family 2. Our results confirm that GPR143 is the major locus for OA1 and that exon 2 is a region of high susceptibility to deletions. Finally, we emphasize the quantitative polymerase chain reaction as a valid tool for diagnosis of deletions in the GPR143 gene.