Purpose To evaluate the diagnostic potential of PET/MRI with 18 FFDG in recurrent ovarian and cervical cancer in comparison to PET/CT. Methods A group of 19 patients with suspected recurrence of pelvic malignancies (ovarian cancer, 11 patients; cervical cancer, 8 patients) scheduled for an 18 FFDG PET/CT were subsequently enrolled for a PET/MRI. The scan protocol comprised: (1) a T1-W axial VIBE after contrast agent adminstration, (2) an axial T2-W HASTE, (3) a coronal TIRM, (4) an axial DWI, and dedicated MR sequences of the female pelvis including (5) a T1-W VIBE before contrast agent adminstration, (6) a sagittal T2-W TSE, and (7) a sagittal T1-W dynamic VIBE. The datasets (PET/CT, PET/MRI) were rated separately by two readers regarding lesion count, lesion localization, lesion conspicuity (four-point scale), lesion characterization (benign/malignant/indeterminate) and diagnostic confidence (three-point scale). All available data (histology, prior examinations, PET/CT, PET/MRI, follow-up examinations) served as standard of reference. Median values were compared using the Wilcoxon rank sum test. Results Metastatic lesions were present in 16 of the 19 patients. A total of 78 lesions (malignant, 58; benign, 20) were described. Both PET/CT and PET/MRI allowed correct identification of all malignant lesions and provided equivalent conspicuity (3.86 ± 0.35 for PET/CT, 3.91 ± 0.28 for PET/MRI; p  > 0.05). Diagnostic confidence was significantly higher for PET/MRI in malignant ( p  < 0.01) and benign lesions ( p  < 0.05). Conclusion Both PET/CT and PET/MRI offer an equivalently high diagnostic value for recurrent pelvic malignancies. PET/MRI offers higher diagnostic confidence in the discrimination of benign and malignant lesions. Considering the reduced radiation dose and superior lesion discrimination, PET/MRI may serve as a powerful alternative to PET/CT in the future.