Diet processing impacts on starch properties, such as the degree of starch gelatinization. This affects digestibility, as shown in laboratory mice fed either a pelleted or an extruded diet. In the present study, the morphology of starch particles throughout the digestive tract of mice was visualized. Thirty-two female C57BL/6J mice were used for a feeding trial. They were fed a commercial maintenance diet for laboratory mice, which was available in pelleted and extruded form, for seven weeks. The mice were sacrificed after the feeding period, and chyme samples were collected from five sites (stomach, anterior and posterior small intestine, caecum, colon). Samples of diets, chyme and faeces were analyzed via stereomicroscopy (stained with Lugol’s iodine) and scanning electron microscopy (SEM). The starch granules appeared more compact in the pelleted diet, showing first signs of degradation only in the small intestine. The caecum content of both diets group was intensively stained, particles as well as fluid phase, indicating that it contained mainly starch. The SEM pictures of caecum content showed abundant bacteria near starch particles. This suggests selective retention of prae-caecally undigested starch in the murine caecum, likely the site of microbial fermentation.