Autosomal dominant iridogoniodysgenesis anomaly (IGDA) is characterized by iris hypoplasia and goniodysgenesis with frequent juvenile glaucoma. IGDA is the result of aberrant migration or terminal induction of the neural crest cells involved in the formation of the anterior chamber of the eye. After eliminating candidate regions for other ocular disorders, a genome-wide scan for IGDA was performed using linkage analysis. Approximately 95% of the genome was excluded with >300 microsatellite markers before significant linkage was demonstrated between IGDA and chromosome 6 markers in two families. From haplotype analysis and identification of recombinants, the IGDA locus is mapped to an 8.3-cM interval distal to D6S477, at 6p25. Our linkage results are consistent with the ocular findings in rare cases of individuals with chromosomal anomalies involving deletions of 6p. This suggests that there is a major gene involved in eye anterior segment development at 6p25.