Background: functional gastrointestinal disorders (FGID) are common conditions in children and adults, often associated with abnormalities of whole gut transit. Currently, transit tests can be performed using several imaging methods, including tracking of radiopaque markers, gamma scintigraphy with the use of radioisotopes, magnetic tracking methods, tracking of movement of wireless motility capsules, and emerging magnetic resonance imaging (MRI) approaches. Objectives: to review recent literature on diagnostic imaging techniques used to investigate whole gut transit in FGIDs. Methods: a systematic review was carried out. The different techniques are described briefly, with particular emphasis on contemporary literature and new developments, particularly in the field of MRI. Conclusions: emerging MRI capsule marker methods are promising new tools to study whole gut transit in FGIDs.