Purpose To compare the diagnostic performance of 18-FDG-PET/MR and PET/CT for the N-and M-staging of breast cancer. Methods and materials Two independent readers blinded to clinical/follow-up data reviewed PET/MR and PET/CT examinations performed for initial or recurrent breast cancer staging in 80 consecutive patients (mean age = 48 ± 12.9 years). The diagnostic confidence for lesions in the contralateral breast, axillary/internal mammary nodes, bones and other distant sites were recorded. Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) were calculated. The standard of reference included pathology and/or follow-up > 12 months. Results Nine of 80 patients had bone metastases; 13/80 had other distant metastases, 44/80 had axillary, 9/80 had internal mammary and 3/80 had contralateral breast tumours. Inter-reader agreement for lesions was excellent (weighted kappa = 0.833 for PET/CT and 0.823 for PET/MR) with similar reader confidence for the two tests (ICC = 0.875). In the patient-perpatient analysis, sensitivity and specificity of PET/MRI and PET/CT were similar (p > 0.05). In the lesion-per-lesion analysis, the sensitivity of PET/MR and PET/CT for bone metastases, other metastases, axillary and internal mammary nodes, contralateral tumours and all lesions together was 0.924 and 0.6923 (p = 0.0034), 0.923 and 0.923 (p = 1), 0.854 and 0.812 (p = 0.157), 0.9 and 0.9 (p = 1), 1 and 0.25 (p = 0.083), and 0.89 and 0.77 (p = 0.0013) respectively. The corresponding specificity was 0.953 and 1 (p = 0.0081), 1 and 1 (p = 1), 0.893 and 0.92 (p = 0.257), 1 and 1 (p = 1), 0.987 and 0.99 (p = 1) and 0.96 and 0.98 (p = 0.0075) respectively. Conclusions Reader confidence, inter-reader agreement and diagnostic performance per patient were similar with PET/MR and PET/CT. However, for all lesions together, PET/MR had a superior sensitivity and lower specificity in the lesion-per-lesion analysis. Key Points • N and M breast cancer staging performance of PET/MR and PET/CT is similar per patient. • In a lesion-per-lesion analysis PET/MR is more sensitive than PET/CT especially for bone metastasis. • Readers' diagnostic confidence is similar for both tests.