Purpose: This study was intended to investigate the migrating motor complex (MMC) changes after ileal bypass in ex-vivo mouse models. Methods: Partial (side-to-side) and total bypass (occlusion of proximal part of bypassed loop) were performed on ileums of female Institute of Cancer Research mice. After 2 and 4 weeks, the bypassed segments were harvested and MMCs were recorded at 4 different sites ex-vivo. Amplitude, duration, interval, direction of propagation, and the area under the curve (AUC) of MMCs were measured and compared to those of the controls. Results: In control mice (n = 7), most MMCs propagated aborally (91.1%). After 2 weeks of partial bypass (n = 4), there was a significant decrease in both amplitude and AUC, and orally-propagating MMCs increased significantly (45%, P = 0.002). Bidirectional MMCs (originating in the bypassed loop and propagating in both directions) were also observed (10%). The amplitude of the MMCs remained decreased at 4 weeks after partial bypass (n = 4), and neither the AUC nor the direction of propagation showed significant changes compared to 2 weeks. Similarly, in the total bypass model, both the amplitude and AUC of the MMCs decreased significantly compared to controls. In contrast to partial bypass, 95% of the MMCs within the bypassed loop propagated aborally after 2 weeks (n = 6), which was similar to the control state. After 4 weeks (n = 5), however, MMCs either lost their temporal relationship or completely disappeared. Conclusion: The changes in propagation direction of the MMCs in the partially bypassed loop may contribute to stagnation of bowel contents and the development of blind loop syndrome.