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The aim of the study was to evaluate the diagnostic accuracy and clinical aspects of 11C-choline and 18F-choline PET/computed tomography (CT) in patients with prostate cancer. A meta-analysis of original studies from 1998 to September 2013 that described choline PET/CT scans for prostate cancer was conducted. We assessed the main sites of positive findings and the relationship between positive findings and histology, change of treatment and serum prostate-specific antigen (PSA) response to the changed treatment. A total of 3167 patients from 47 eligible articles were assessed with respect to their findings on choline PET/CT during staging and restaging for biochemical recurrence. We examined 661 patients at staging and 158 patients at restaging for biochemical recurrence after external beam radiotherapy. These patients had positive results in the prostate bed more often than did the 2348 patients with biochemical recurrence after radical prostatectomy (P<0.001, χ2-test). On assessing 609 patients, the pooled sensitivity of choline PET/CT for pelvic lymph node metastases was found to be 0.62 [95% confidence interval (CI) 0.51–0.66] and the pooled specificity was found to be 0.92 (95% CI 0.89–0.94). Head-to-head studies of 280 patients showed that more patients had positive findings with choline PET/CT than with bone scanning [127 (45%) vs. 46 (16%), odds ratio 2.8, 95% CI 1.9–4.1, P<0.0005, Wilcoxon rank test]. Choline PET/CT led to a change in treatment in 381 (41%) of 938 patients. The changes yielded complete PSA response in 101 of 404 (25%) patients. 11C-choline or 18F-choline PET/CT is useful as the first imaging examination for patients with prostate cancer and biochemical recurrence with PSA levels between 1.0 and 50 ng/ml.