Capsule-based methods for assessment of gastrointestinal (GI) motility have seen great improvements in recent decades. The most recent development is the electromagnetic Motilis 3D-Transit system (3D-Transit). The aim of this paper is to review and discuss the development and technical properties of magnetic tracking of GI motility. We performed a comprehensive literature review on magnetic tracking in GI research. The motility tracking system was the first capsule-based magnetic system to be used in GI motility research. However, the potential of the system was hampered by its stationary and hospitalizing nature. This led to the development of the electromagnetic Motilis 3D-Transit system. The 3D-Transit system is a portable system that allows for assessment of both whole gut and regional transit times and contraction patterns in a fully ambulatory setting in the patients' home environment with only minor restrictions on movements. The spatiotemporal resolution of 3D-Transit allows assessment of segmental colonic transit times and permits an analysis of gastric and colonic movements with a degree of detail unrivalled by other ambulatory methods, such as the wireless motility capsule. Recently, robust normative data on 3D-Transit have been published. This review provides a current perspective on the use of capsule-based magnetic tracking systems in GI research and how they represent a potentially valuable clinical resource for GI physicians and in GI research.