Abstract Introduction/Purpose Weight regain and weight loss failure after bariatric surgery are important issues that may require a weight regain procedure. Three-dimensional-computed tomography (3D-CT) is a well-established method allowing exact measurements of pouch volume. The aims of this study were to prove the applicability of swallow MRI as a non-ionizing procedure and compare it to 3D-CT in patients after weight regain procedures following RYGB. Materials and Methods Twelve post-RYGB patients who had a follow-up operation for weight regain before 12/2017 were included in this prospective study. Swallow MRI and 3D-CT were performed in each patient to evaluate the size of the anastomosis, pouch volume, and intrathoracic pouch migration (ITM). Results Mean pouch volume in swallow MRI and 3D-CT were 40.4 ± 21.0 ml and 43.5 ± 30.2 ml, respectively (p = 0.83), and pouch diameter at the maximal distention was 35.3 ± 5.9 ml (MRI) and 31.0 ± 10.0 ml (CT) (p = 0.16). The rate of ITM was 75% in both examinations (p = 1.0). Conclusion Swallow MRI is a valid method for the assessment of pouch volume in different phases of the swallowing process and is comparable to 3D-CT. The diagnosis of ITM using swallow MRI was equal to 3D-CT.