Background In mammals, starch is digested mostly in the small intestine. However, most in vivo starch digestion studies have been carried out using digesta from terminal ileum, colon, and feces, and thus cannot give unambiguous information on starch digestion in the small intestine. Furthermore, many in vitro studies have tried to stimulate the digestion in the small intestine without reference to in vivo studies of starch digestion in the small intestine. Therefore, current in vitro methods might not reflect in vivo digestion. Objective This study explores the in vivo starch digestion in the pig small intestine and compares it with a standard in vitro method. Design Digesta were collected from different sections of small intestine of seven pigs fed with a diet containing 47% (dry weight basis) raw normal maize starch. Starch contents of the digesta were analysed using Megazyme total starch kits. The pig diet was also digested using a modified in vitro method (Sopade and Gidley, Starch, 2009, 61, pp. 245). Starch was extracted from the in vivo and in vitro digesta following the method of Syahariza et al. (Carbohydr. Polymers, 2010, 82, pp. 14) and analyzed using size exclusion chromatography (SEC, fully branched and debranched using isoamylase) following the methods of Witt et al. (J. Agric. Food Chem., 2010, 58, pp 8444). Outcomes The starch digestion in mouth and stomach was minor compared with that in the small intestine, and raw normal maize starch was almost completely digested in the first half of the small intestine. The time evolution of the size distributions (fully branched and debranched) of starch molecules during in vivo and in vitro digestion analyzed using SEC showed a qualitative difference between the two digestion methods. The former showed a degradation of starch molecules to a more uniform size, whereas the latter show a complex mechanism, which preserved the size distribution of native starch at the beginning of the digestion before producing a multimodal distribution. Conclusion The heterogeneous nature of the in vivo digestion cannot be reproduced by current in vitro methods, which are more homogenous. Nutritional claims of starch products based on in vitro methods need to take account of this phenomenon. Source of funding This study is financially supported by the Australian Research Council (DP0985694). The small intestine digesta were provided by the High Fibre Grains Cluster (supported by a grant from the CSIRO Flagship Collaboration Fund via the Food Futures Flagship)