A combined (19)F and (1)H MRI framework for the assessment of human intestinal transit and motor function is presented. This framework consists of silicone coated polychlorotrifluoroethylene capsules filled with perfluoro--crown-5-ether as (19)F marker, a flexible (19)F surface coil and a (19)F projection imaging sequence, allowing for real-time tracking of a single or multiple capsules. The capsules (length 11.5 mm, Ø 7.2 mm) contain 140 μL perfluoro--crown-5-ether and were tested for cytotoxicity and leakage prior to oral administration. A balanced SSFP projection sequence was implemented, yielding a temporal resolution of 133 ms. Optional multi-frequency excitation, allowing for interleaved tracking of differently labeled (19)F capsules, was incorporated. The passage of the (19)F capsules through intestinal sections was monitored in two healthy volunteers. Capsule coordinates were successfully coregistered with anatomical reference scans. Intestinal motility, residence times, lengths and forward velocities were determined. Simultaneous tracking of two capsules allowed for the assessment of peristaltic patterns with correction for respiratory motion. By providing the means for real-time multiple capsule tracking and high resolution anatomical imaging, the presented multinuclear imaging framework has the potential to provide important supplemental information for physiological and pharmaceutical research.