In people, cisapride was found to cause a certain type of heart rhythm disorder, or arrhythmia, called QT-interval prolongation, and so it was removed as a commercially available medication. Otherwise, its side effects were found, even in people, to be fairly minimal.
This arrhythmia effect has not been documented in veterinary patients, and since it does appear to be very beneficial for cats with megacolon and some cases of constipation, it can still be prescribed through a veterinary compounding pharmacy.