Objective To use meta-analysis method to assess the efficacy of fluorine-18fluorode-oxyglucose positron emission tomography/computed tomography (PET/CT) (18F-FDG-PET/CT) scan and 99Tcm-methylene diphosphonate (99Tcm-MDP) bone scan (BS) on early diagnosis of bone metastases of cancer. Methods Computer-based retrieval was conducted on MEDLINE, PubMed, EMbase, Ovid, and The Cochrane Library (from their establishment to 2010) to search reports about diagnosing bone metastases of cancer with 18FDG-PET/CT and 99Tcm-MDP Bone Scan. Three reviewers independently selected the studies according to the inclusion and exclusion criteria, collected the data, and evaluated the quality. MetaDisc software was adopted to conduct meta-analyses. The pooled sensitivity, specificity, and diagnostic odds ratio (DOR) were calculated, the summary receiving operating characteristic (SROC) curve was drawn, and the areas under the curve (AUC) and Q were measured. Results Five studies were included. The results of meta-analyses showed that the pooled sensitivity of 18FDG-PET/CT and 99Tcm-MDP BS in the diagnosis of bone metastases was 0.95 (95%CI 0.90 to 0.97) and 0.77 (95%CI 0.71 to 0.83), respectively; the pooled specificity was 0.98 (95%CI 0.97 to 0.99) and 0.90 (95%CI 0.88 to 0.92), respectively; the pooled DOR was 602.81 (95%CI 214.07 to 1697.51) and 41.37 (95%CI 8.15 to 210.05), respectively; the AUC was 0.984 2 and 0.901 7, respectively; and the Q index was 0.945 4 and 0.833 1, respectively. Conclusion The 18F-FDG PET/CT is more effective than the 99Tcm-MDP bone scan in the early diagnosis of bone metastases in cancer.