Magnetic resonance imaging (MRI) is a versatile medical imaging tool for which several new applications have been developed. Beside its broad clinical use for the detection of anatomical structures and pathologies MRI has been successfully applied for the non-invasive imaging of human organ functions, including the brain and the cardiovascular system. The use of MRI for the assessment and analysis of gastrointestinal (GI) function is a new approach that is currently performed in only a few research sites. Several characteristics make MRI an ideal technique for the direct assessment of GI physiology: MRI acquires high resolution images with excellent soft tissue contrast, it does not expose subjects to ionizing radiation, is non-invasive, and the acquisition and analysis of the images can be independently verified. In this article we summarize recent developments of MRI techniques in GI research. We will also discuss the advantages and limitations of MRI for this purpose in relation to established medical imaging tools and investigations.