Purpose: Bowel toxicity can be difficult to manage in the treatment of abdominal cancers. The bowel experiences large motion during treatment, causing it to enter high‐dose regions. Real‐time MR imaging during radiotherapy allows for potential visualization and dosimetric avoidance of the bowel during treatment. To investigate the feasibility of real‐time ‘bowel‐gated’ treatment using onboard MRI, we assessed two bowel‐tracking algorithms on 32 cine imagesets acquired with the ViewRay hybrid MR‐ radiotherapy unit. Methods: The Viewray(TM) System, which is an integrated 0.35T MR‐Co‐60 system that is pending 510k approval, was used to acquire 32 cine image sets in 5 patients under an IRB‐approved trial. Each imageset was acquired in 2D (coronal or sagittal orientation) for an average duration of 0.5‐2.5 minutes at a frame rate of 4 frames/s. The initial position of the bowel was manually contoured on the first image frame. Two algorithms were evaluated in tracking bowel from its initial position throughout its motion for the duration of the cine set ‐ a normalized cross‐ correlation (NCC) algorithm, and a weighted NCC (WNCC) algorithm. To assess the tracking feasibility and accuracy of these two methods, the initial contour was virtually shifted with the tracked motion and displayed on tracked cine images. The agreement between the shifted contour and the border of the bowel was manually inspected and noted for each frame. Results: Both algorithms successfully tracked 31/32 cases in 100% of frames. The WNCC algorithm outperformed the NCC algorithm in speed, with a mean processing speed of.007s versus.013s, respectively, and captured a greater range of motion in all cases. Conclusions: The demonstrated feasibility of bowel tracking on cine MR imagesets indicates its potential successful use in real‐time bowel tracking and gated radiotherapy. While both algorithms performed well, the WNCC algorithm was superior in processing speed and sensitivity to bowel motion.