Internally brown (IB) tomato fruit is a physiological disorder in which the inside of the fruit turns brown or black. The mechanisms underlying the development of IB are not well understood. In this study, we examined the incidence of IB using hydroponics, and investigated the anatomical features and the ratio of dimeric rhamnogalacturonan II-borate (dRG-II-B) to total rhamnogalacturonan II (RG-II) (boron cross-linking ratio) in cell walls that decreased with boron deficiency. IB fruit developed when the growth of the stem and leaves were normal and the micro-element concentrations were low. The IB region was observed to be brown inside the fruit at an early stage, and this changed to black in the mature fruit. It was detected around the pericarp, locular gel, placenta and columella in the tomato fruit. An abnormality was observed around the vascular bundle in IB fruit. The interior of the cells near the vascular bundle was changed to a substance with a high electron density, and a disintegrated image was observed. Few Ca precipitates were observed on plasma membranes or cell walls in the collapsed cells by an antimonite precipitation method. It is suggested that Ca deficiency appears to be related to the cell collapse in IB. There was no significant difference in the boron cross-linking ratio between the IB and normal fruit. This suggested that IB was not related to B deficiency directly. We concluded that IB was caused by necrosis of cells around the inner vascular bundle due to Ca deficiency.