Previous studies have shown that short CAG repeats in the androgen receptor (AR) gene are associated with increased risk of prostate cancer. It is unclear if this association is due to linkage disequilibrium with a susceptibility locus or directly linked to the possible functional impact of the length of the CAG repeats. In this study, the number of the AR CAG repeats was determined in prostate cancer patients, benign prostatic hyperplasia (BPH) patients, and controls in both Swedish and Japanese men. Prostate cancer patients included 59 Swedish hereditary, 59 Swedish sporadic and 33 Japanese sporadic cases. BPH patients included 38 Swedish and 33 Japanese cases. Controls included 98 Swedish healthy men and 43 Japanese men without either prostate cancer or BPH. No significant difference in AR CAG repeats was found in comparison between BPH patients and controls. In contrast, both Swedish hereditary and sporadic prostate cancer patients had shorter AR CAG repeats than Swedish controls, but Japanese prostate cancer patients had longer repeats than controls. These differences between the two populations in the association of prostate cancer and the AR CAG repeats may suggest that the AR CAG repeats are in linkage disequilibrium with a prostate cancer susceptibility locus localized in a small region flanking or overlapping the AR gene at Xq12.1.