Various botanical and structural characteristics of starchy foods are considered to modify the rate of starch digestion and the glycaemic responses in humans. The main objective of the study was to examine the impact of fermented barley and oat microstructure on the rate of in vitro starch hydrolysis. A dynamic gastrointestinal model was used to estimate the degree of starch hydrolysis during in vitro digestion of fermented whole grain cereal meals. Light microscopy and confocal laser scanning microscopy were used to study the microstructural changes. In parallel to the in vitro studies, the impact of fermented barley and oats on postprandial plasma glucose responses was evaluated in a human study. Micrographs were taken during in vitro digestion experiments with fermented whole grains and compared with micrographs of boiled barley (undigested). Images showed that most of the oat starch granules were degraded after 120 min of digestion, whereas barley starch granules were less degraded, even after 180 min of digestion. The findings were confirmed by faster starch hydrolysis from the fermented oat meal, measured as maltose generated during in vitro digestion. The area under the curve (AUC) was calculated from the plotted maltose curves of the meals. AUC for barley tempe (266 ± 33) was 40 % of the AUC for oat tempe (663 ± 8) and significantly different (p < 0.007) from AUC oat tempe. The in vitro data closely resembled the AUCs for plasma glucose from the parallel human study. In terms of glucose response, the mean AUC for barley tempe was 46 % of the AUC for oat tempe in the human study. The agreement between the in vitro and in vivo data indicates the potential of the in vitro method as a tool to predict the rate of starch degradation of cereal products.