The time evolution of the size distributions of (fully branched and debranched) starch molecules during in vivo and in vitro digestion was analyzed using size exclusion chromatography (SEC) and compared. In vivo digesta were collected from the small intestine of pigs fed with raw normal maize starch; in vitro digestion was carried out on the same diet fed to the pigs using a method simulating digestion in the mouth, stomach, and small intestine. A qualitative difference was observed between the in vitro and the in vivo digestion. The former showed a degradation of starch molecules to a more uniform size, whereas the in vivo digestion preserved the size distribution of native starch before producing a multimodal distribution, the heterogeneous nature of which current in vitro methods do not reproduce. The use of in vitro digestion to infer in vivo digestion patterns and, hence, potential nutrition benefits need to take account of this phenomenon.