The need for an efficient linkage analysis strategy for autosomal dominant poycystic kidney disease (ADPKD) is rather increasing after the cloning of major responsible gene, PKD2, with large and complex gene structure. In general, markers for linkage study should have high heterozygosity, proximity to the disease locus, and productivity. To meet these requirement, we applied the high-throughput genotyping strategy using microsatellite markers to analyze linkage to PKD1. From the marker detabase of Cooperative Human Linkage Center, one intragenic (UTR.05049_L33243), two distal (D16S521, D16S3024), and two proximal (D16S3027, D16S423) markers were chosen for this evaluation. Genomic fragments including dinucleotide repeats were amprified with fluorescent-primers, and the sizes of the fragments were evaluated using ABI Prism 377 and GeneScan software. Heterozygosity of each marker was calculated based on the 100 genotypes obtained from 50 normal Japanese population. UTR_05049_L33243, as well as another intragenic polymorphic marker, KG8, had low heterozygosity (0.45 and 0.36, respectively). Three of the four neighboring markers, D16S3024, D16S3027, D16S423, had high heterozygosity (>0.80). In addition, three Japanese families inheriting ADPKD were analyzed for linkage to PKD1. LOD score tables were made using FASTLINK software. Two families were positively linked to PKD1, whereas the other one was unlinked. We conclude that high-throuput genotyping using D16S3 024, D16S3027, and D16S423 is very useful in the linkage analysis of ADPKD.