The purpose of this study was to assess the diagnostic accuracy of whole-body MRI (WB-MRI) at 1.5 T or 3 T compared with FDG-PET-CT in the follow-up of patients suffering from colorectal cancer. In a retrospective study, 24 patients with a history of colorectal cancer and suspected tumour recurrence underwent FDG-PET-CT and WB-MRI with the use of parallel imaging (PAT) for follow-up. High resolution coronal T1w-TSE and STIR sequences at four body levels, HASTE imaging of the lungs, contrast-enhanced T1w- and T2w-TSE sequences of the liver, brain, abdomen and pelvis were performed, using WB-MRI at either 1.5 T (n = 14) or 3 T (n = 10). Presence of local recurrent tumour, lymph node involvement and distant metastatic disease was confirmed using radiological follow-up within at least 5 months as a standard of reference. Seventy seven malignant foci in 17 of 24 patients (71%) were detected with both WB-MRI and PET-CT. Both investigations concordantly revealed two local recurrent tumours. PET-CT detected significantly more lymph node metastases (sensitivity 93%, n = 27/29) than WB-MRI (sensitivity 63%, n = 18/29). PET-CT and WB-MRI achieved a similar sensitivity for the detection of organ metastases with 80% and 78%, respectively (37/46 and 36/46). WB-MRI detected brain metastases in one patient. One false-positive local tumour recurrence was indicated by PET-CT. Overall diagnostic accuracy for PET-CT was 91% (sensitivity 86%, specificity 96%) and 83% for WB-MRI (sensitivity 72%, specificity 93%), respectively. Examination time for WB-MRI at 1.5 T and 3 T was 52 min and 43 min, respectively; examination time for PET-CT was 103 min. Initial results suggest that differences in accuracy for local and distant metastases detection using FDG-PET-CT and WB-MRI for integrated screening of tumour recurrence in colorectal cancer depend on the location of the malignant focus. Our results show that nodal disease is better detected using PET-CT, whereas organ disease is depicted equally well by both investigations.