Introduction Organic acids from plant food have been shown to play an important role in the prevention of chronic diseases (osteoporosis, obesity), inherent to western diets, but little is known about their bioavailability in the small intestine, information that needs to be determined in order to quantify likely effects on human health. Methods An in vitro model of human digestion was carried out, comprising simulated oral, gastric and pancreatic digestion followed by an in vitro model of small intestine absorption using Caco-2 cell monolayers. As models for fruits and vegetables, freeze-dried or raw samples of banana and sweet potato were used. Results Organic acids have been found to be slowly released from the food matrix during simulated digestion of both banana and sweet potato, either raw or after freezedrying. In the Caco-2 cell assay, malic and oxalic acids were absorbed more than citric acid. Oxalic and citric acids, but not malic acid, were transported across the cell monolayer. The release and uptake of major organic acids from model fruits and vegetables using established in vitro simulation processes was not quantitative and varied with acid type.Conclusion Partial uptake is consistent with a dual nutritional role for organic acids as alkalinising agents (fraction which is taken up) and as modulators of large intestinal function (fraction which is not taken up in the small intestine). Studies of in vivo digestive release and uptake are needed in order to identify the contribution of organic acids to the nutritional value of fruits and vegetables.