Objective To compare the accuracy of 18F-FDG and 11C-choline PET/CT in diagnosis of prostate cancer. Methods This prospective study enrolled 63 consecutive patients with prostate diseases and presenting with rising PSA. All had 11C-choline and 18F-FDG PET/CT performed, maximum standardized uptake value SUV was used for image evaluation. The result of 11C-choline and 18F-FDG PET/CT were compared with pathologic findings, sensitivity, specificity, positive predictive value, negative predictive value were calculated for both the tracers. Possible correlation between serum prostate specific antigen(PSA)and SUVmax were investigated with linear correlation. Results (1)11C-Choline SUVmax difference was statistically significant between the patients with prostate cancer and benign lesions (P<0.01),but there were no statistically significant differences of 18F- FDG SUVmax among two groups (P>0.05). Two groups, fPSA (ng/mL) were statistically significant difference (P<0.05). (2)18F-FDG SUVmax were positively correlated with f/T ratio in prostate cancer patients (r=0.474, P<0.05),but were negatively correlated with serum f/T ratio in patients with prostatic benign lesions (r=0.540, P<0.05). Conclusion In our experimental conditions, 11C-choline provided a statistically better performance in terms of lesion detection rate as compared with 18F-FDG, but 18FFDG and 11C-choline PET/CT play a complementary role in the diagnosis of prostate cancer patients, fPSA and serum f/T also can assist in making the diagnosis．