New generation SPECT/CT scanners allow rapid whole-body imaging, and potentially facilitate significantly improved diagnostic accuracy. Thus, the aim of this study was to compare the diagnostic accuracy of whole-body Tc-99m-HDP SPECT/CT, F-18-FDG PET/CT, and their combination for detecting bone metastases in breast cancer. Women with biopsy-proven breast cancer that were referred for whole-body SPECT/CT and FDG PET/CT were consecutively included in this retrospective study. Two blinded readers independently interpreted all scans. In a per-patient analysis, the diagnostic performances of whole-body SPECT/CT, FDG PET/CT, and their combination were compared using receiver operating characteristic (ROC) analysis. In a per-lesion analysis, the performances were compared using figures of merit (FoM) differences in Jackknife alternative free-response ROC analysis, which considers the location information. Follow-up served as reference standard. Overall, 25 consecutive women (median age: 55; range 38-82) with 117 lesions were included. The median follow-up was 21 months (2-46 months). The per-patient analysis revealed no significant differences in diagnostic performance (P = 0.16), while the per-lesion analysis revealed a diagnostic superiority of whole-body SPECT/CT over FDG PET/CT (P = 0.004). Specifically, the PET/CT FoM was significantly lower than the SPECT/CT FoM (FoM difference = -0.11, 95% CI [-0.21; -0.02], P = 0.021). No significant difference was observed between SPECT/CT and the combination of SPECT/CT and PET/CT. The per-lesion analysis suggest that SPECT/CT has a higher diagnostic accuracy than FDG PET/CT for the detection of bone metastases. Thus, SPECT/CT may be a useful adjunct to FDG PET/CT for staging of breast cancer patients.