We prospectively assessed and compared the usefulness of 11C-choline positron emission tomography (PET) with that of [18F]-2-fluoro-2-deoxy-D-glucose (FDG) PET for the differentiation between benign and malignant tumors. A total of 126 patients with 130 lesions were studied (25 brain tumors, 51 head and neck tumors, 15 bone tumors, 16 lung tumors, and 23 soft tissue tumors). 11C-choline PET and FDG PET were performed from 5 and 40 min, respectively, after injection of 275-370 MBq tracer. PET data were evaluated using the standardized uptake value (SUV) and were analyzed in accordance with the pathologic data. The 11C-choline uptake in malignancies was 3.9+/-2.3 (n=81), which was significantly higher than that in benign lesions (n=49) (2.6+/-1.7, P<0.005). The FDG uptake in malignancies was 5.9+/-3.8 (n=81) and was also significantly higher than that in benign lesions (2.8+/-2.0, P<0.0001). The 11C-choline uptake in the lesions correlated with FDG uptake (r=0.65, P<0.003). According to an ROC analysis, the areas under the ROC curves (AUCs) for 11C-choline PET were more than 0.8 in bone, head and neck, lung, and soft tissue tumors, while the AUC was 0.79 in brain tumors. The AUCs for FDG PET were similarly more than 0.8 in bone, head and neck, lung, and soft tissue tumors, but had a lower value of 0.585 in brain tumors. In brain, head and neck, bone, and soft tissue tumors, 11C-choline showed higher contrast than FDG. In conclusion, it is feasible to use 11C-choline PET for differentiation between malignant and benign tumours, especially of the brain, head and neck, bone, and soft tissue. However, attention needs to be drawn to the high uptake of 11C-choline in some benign tumors and tumour-like lesions, as this will be of significance in clinical practice.