This pilot prospective evaluation study is to verify the efficiency of (18)F-Alfatide II, a specific PET imaging agent for integrin αvβ3, in detecting bone metastasis in human, with comparison to (18)F-FDG PET. Thirty recruited patients underwent (18)F-FDG and (18)F-alfatide II PET/CT successively within days. The final diagnosis of bone lesions was established based on the comprehensive assessment of all available data and clinical follow-up, which fall into four groups: osteolytic, osteoblastic, mixed and bone marrow. Visual analysis and quantification of SUVmax were performed to compare the detection sensitivity of (18)F-Alfatide II and (18)F-FDG PET. Eleven patients were found to have a total of 126 bone metastasis lesions. (18)F-Alfatide II PET can detect the bone metastatic lesions with good contrast and higher sensitivity (positive rate of 92%) than (18)F-FDG PET (77%). Especially, (18)F-Alfatide II PET showed superiority to (18)F-FDG PET in detecting osteoblastic (70% vs. 53%) and bone marrow metastatic lesions (98% vs. 77%). In conclusion, (18)F-Alfatide II PET/CT can be used to detect skeletal and bone marrow metastases, with nearly 100% sensitivity in osteolytic, mixed and bone marrow lesions. The sensitivity of (18)F-Alfatide II PET/CT in osteoblastic metastases is relatively low but still significantly higher than that of (18)F-FDG PET/CT. This pilot clinical study warrants the further application of (18)F-Alfatide II PET/CT in metastatic lesion detection, patient management and drug therapy response monitoring.