PAX2 is one of nine PAX genes that have been described in vertebrates. Each PAX gene contains a conserved paired box domain that was first identified in Drosophila. PAX2 encodes a transcription factor that has a critical role in the development of the urogenital tract, the eyes, and the CNS. Recently, we reported a mutation of PAX2 in patients with optic nerve coloboma, vesicoureteric reflux, and renal anomalies. To facilitate further analysis of PAX2 mutations in human disease, we have now determined the complete structure of the human PAX2 gene. Five genomic lambda clones containing human PAX2 gene sequences were isolated. Sequencing and restriction mapping of these clones showed that human PAX2 was composed of 12 exons spanning approximately 70 kb. Two alternatively spliced exons and a dinuclotide repeat polymorphism were also determined in PAX2. These data will be useful in characterizing the role of PAX2 in human disease.