Magnetic resonance imaging (MRI) was used to monitor internal changes in harvested tomato (Solanum lycopersicum L. cv. Micro-Tom) fruit. Measurements of ethylene evolution, respiration, and ion leakage indicated that the fruit developed chilling injury (CI) after storage at 0. °C. Unlike these measurements, MRI provided spatially resolved data. The apparent diffusion coefficient (ADC), which is an indication of water mobility in tissues, was calculated from MRIs of the different parts of the fruit. Storage for 1 or 2 weeks at 0. °C caused no difference in the ADCs (D-values) in the pericarp, but it did lead to higher values in the inner tissues i.e., the columella and locular region compared to non-chilled fruit (P< 0.05). Changes in inner fruit D-values after 1 and 2 weeks of chilling at 0. °C were similar to changes in respiration, ethylene production and ion leakage which increased (P< 0.05) compared to the non-chilled controls. Most CI studies of tomato fruit used pericarp tissue. Our data indicate that columella tissue changes occur in response to chilling injury in tomato fruit and suggest that more caution is needed when interpreting data from experiments commonly used to study this phenomenon. © 2014 Elsevier B.V.