Starch gelatinization is a major determinant of carbohydrate digestibility and varies with diet processing. Laboratory rodent diets are often marketed as identical, but are sold in different forms, regardless of the markedly higher starch gelatinization in extruded than in pelleted diets. Our hypothesis was that this would impact energy and nutrient digestibility in mice fed pellets or extrudate, respectively. Trial 1 showed that feeding C57BL/6 mice a standard maintenance diet in extruded form results in a significantly higher digestibility of organic matter, energy, and carbohydrates than the identical diet in pelleted form. The replication of the experiment, however, revealed a variation between batches of the same pelleted diet regarding starch and total dietary fiber contents. Given the significant differences in diet digestibility and the potential impacts of digestibility on nutrient utilization, the intestinal microbiome, and intermediary metabolism, trials performed with differently processed diets are not comparable. This might partly explain failures to reproduce results, especially in gastrointestinal or microbiome research. Considering this impact on experimental animals, the degree of starch gelatinization should be declared in the diet information for laboratory animal diets. The differences between batches of laboratory animal diets as observed in the pellets are not acceptable.