A major challenge for the management of prostate cancer (PCa) patients is to predict the clinical course of the disease after radical prostatectomy. A previous comprehensive immunohistochemical analysis using an automated image analyzer suggested that prolyl isomerase Pin1 (hence Pin1) may be a potent predictor of recurrence in PCa patients. However, a detailed pathological standard for evaluating the Pin1 immunohistochemistry in PCa has not been established yet. We here introduce a practical scoring system for Pin1 immunostaining in PCa. Using this method, the immunoreactivity of tumor cell cytoplasm and nucleus was evaluated separately and then scored for four grades (Grade=0-3). We defined the Pin1 score as the sum of both nuclear and cytoplasmic grades (Score=0-6), and the cases were then divided into either a low Pin1 score group (2) or a high Pin1 score group (3). We examined the correlation between this scoring system and postoperative PSA recurrence for 78 PCa patients. PCa patients assigned to the high Pin1 score group demonstrated PSA relapse more frequently than those assigned to the low Pin1 score group (p<0.0001). This suggests that, at the common laboratory level, our Pin1 scoring system could be a useful tool for predicting the prognosis of PCa patients after surgery.