It was reported that 15 of 19 consultation cases of prostatic partial atrophy were a-methylacyl coenzyme A racemase (AMACR)-positive. We investigated partial atrophy cases from a single institution using a standard AMACR immunostaining method. Immunohistochemical analysis was performed using an antibody cocktail containing p63, high-molecular-weight keratin (34bE12), and AMACR antibodies on 122 foci of partial atrophy. AMACR staining was analyzed in partial atrophy (n = 122) and compared with adjacent benign glands (n = 122) and prostatic carcinomas (n = 28). Of 122 foci of partial atrophy, 38 (31.1%) showed AMACR immunoreactivity. Typically, AMACR staining was weak or moderate. In addition, 82 (67.2%) showed patchy to negative distribution of basal cells. Partial atrophy may show AMACR immunoreactivity when using a 34bE12, p63, and AMACR antibody cocktail staining method. Compounding this problem, focal lack of basal cells may be seen. However, the AMACR staining pattern of partial atrophy is usually comparable to that of adjacent benign glands and substantially different from adenocarcinoma.