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High-grade prostatic intraepithelial neoplasia (HGPIN) appears to represent an ideal target for chemoprevention of prostate cancer (PCa). HGPIN responds to androgen ablation and has prostate stem cell antigen (PSCA) mRNA expression. One hundred and seventy two patients with isolated HGPIN were randomized in a double-blind manner to receive flutamide 250 mg/day (86 cases) or a placebo (86 cases) for 12 months and were rebiopsied at 12 and 60 months. PSCA mRNA expression was assessed in the prestudy and 12-month biopsies byin situhybridization. The incidence of subsequent PCa was 11.6% in the flutamide group when compared with 30.2% in the placebo group over a follow-up period of 5 years (p= 0.0027). PSCA mRNA expression levels were significantly declined after treatment compared with that before treatment (p< 0.001). After treatment, 66 patients had reduced PSCA mRNA expression, in whom none was found with cancer on follow-up, however, 13 cases had increased PSCA mRNA expression levels, in whom 11 were found with cancer. Cox regression analysis demonstrated that HGPIN with increased PSCA mRNA expression after flutamide had an increased relative risk of 4.33 to develop subsequent cancer (95% confidence intervals: 2.48–7.36;p< 0.001). Seventeen (19.8%) cases had the flutamide-associated side effects, which were graded as mild, but all did not discontinue study. Flutamide can effectively and safely reduce PCa development and significantly suppress PSCA mRNA expression in men with isolated HGPIN, whereas the increased PSCA mRNA expression after therapy may be a clinically adverse predictor for cancer onset.