This study was performed to prospectively investigate the impact of image fusion in resolving discrepant findings between fluorine-18 fluorodeoxyglucose positron emission tomography (FDG-PET) and magnetic resonance imaging (MRI) or X-ray computed tomography (CT) in patients with gynaecological cancers. Discrepant findings were defined as lesions where the difference between the FDG-PET and MRI/CT images was assigned a value of at least 2 on a 5-point probability scale. The FDG-PET and MRI/CT images were taken within 1 month of each other. Image fusion between FDG-PET and CT was performed by automatic registration between the two images. During an 18-month period, 34 malignant lesions and seven benign lesions from 32 patients who had undergone either surgical excision or a CT-guided histopathological investigation were included for analysis. Among these cases, image fusion was most frequently required to determine the nature and/or the extent of abdominal and pelvic lesions (28/41, 68%), especially as regards peritoneal seeding (8/41, 20%). Image fusion was most useful in providing better localisation for biopsy (16/41, 39%) and in discriminating between lesions with pathological versus physiological FDG uptake (12/41, 29%). Image fusion changed the original diagnosis based on MRI/CT alone in 9/41 lesions (22%), and the original diagnosis based on FDG-PET alone in 5/41 lesions (12%). It led to alteration of treatment planning (surgery or radiotherapy) in seven of the 32 patients (22%). In patients with gynaecological cancers, the technique of image fusion is helpful in discriminating the nature of FDG-avid lesions, in effectively localising lesions for CT-guided biopsy and in providing better surgical or radiotherapy planning.