Autosomal dominant polycystic kidney disease (ADPKD), is an inherited disorder with genetic heterogeneity. The presence of renal cysts is an important clinical marker for ADPKD diagnosis, but in the early stage, renal cysts do not emerge in individuals who carry the defective gene. Therefore, it is necessary to establish a genetic method of diagnosis. Two ADPKD-related genes have been isolated: PKD1, located on chromosome 16p13.3, and PKD2, located on 4q21-22. In this study, we used fluorescent short tandem repeat (STR) markers to perform linkage analysis in six unrelated ADPKD families. Six markers were included in the PKD1 and five in the PKD2 analysis. Among these six ADPKD families, four showed linkage to PKD1 and two showed linkage to PKD2. Ultrasonography or computerized tomography revealed that PKD1 patients developed cysts only in kidneys, but PKD2 patients developed cysts in kidneys, liver and pancreas. Our results indicate that fluorescent STR linkage analysis is well suited for type identification of ADPKD and presymptomatic diagnosis in ADPKD families.