Background: Autosomal dominant polycystic kidney disease (ADPKD) is an inherited disorder with genetic heterogeneity. Up to three loci are involved in this disease, PKD1 on chromosome 16p 13.3, PKD2 on 4q21, and a third locus of unknown location. Methods: Here we report the first molecular genetic study of ADPKD and the existence of locus heterogeneity for ADPKD in the Iranian population by performing linkage analysis on 15 affected families. Results: Eleven families showed linkage to PKD1 and two families showed linkage to PKD2. In two families, PKD1 markers are common in all affected members but PKD2 markers were not informative. Conclusion: The results of this study demonstrate significant locus heterogeneity in autosomal dominant PKD in Iran. Analysis of clinical data confirms a milder ADPKD phenotype for PKD2 families. Our results showed relatively high heterozygosity rates and PIC values for some markers, while the most informative markers were KG8 and 16AC2.5 for PKD1 gene and AFM224x6 for PKD2 gene.