Iris hypoplasia is an autosomal dominant disorder which is frequently associated with glaucoma. This glaucoma is usually resistant to medical therapy and can lead to blindness. A large family of Scandinavian descent with a five generation history of iris hypoplasia was studied. Fifteen individuals were found to have iris hypoplasia, nine of whom had associated glaucoma. In an attempt to identify the chromosomal location of the disease-causing gene, this family was genotyped with short tandem repeat polymorphisms (STRPs) known to map to loci previously associated with glaucoma. The juvenile glaucoma locus at 1q25 and a congenital glaucoma locus on 6p were both statistically excluded. However, significant linkage was demonstrated at the Rieger syndrome locus at 4q25. The highest observed LOD score was 3.70 (theta = 0) and was obtained with marker D4S1616. Three recombination events were observed in affected individuals that together demonstrate that the disease-causing gene lies between markers ACT3E03 and D4S1611, an interval of approximately 7 cM. These results suggest that autosomal dominant iris hypoplasia and Rieger syndrome are allelic.