The germinated seeds of many plants are a natural source of substances that can be used to supplement food and increase its functionality. The seeds’ metabolism may be modified during germination to produce specific health-promoting compounds. Fagopyrum esculentum Moench is a rich source of nutrients. Buckwheat seeds modified during germination may be helpful as an additive to new functional food products with anti-atherogenic properties. However, their effect and safety should be assessed in in vivo studies. The aim of the study was to evaluate the effect that adding modified buckwheat sprouts (Fagopyrum esculentum Moench) to an atherogenic (high-fat) diet has on the morphology and digestibility parameters of rats. Buckwheat seeds were modified by adding the probiotic strain of the yeast Saccharomyces cerevisiae var. boulardii. The study was carried out on 32 Wistar rats, and digestibility and blood counts were assessed during the experiment. There was no evidence of an adverse effect on the animals' weight gain and nutritional efficiency. However, the influence of diets with freeze-dried buckwheat sprouts on digestibility and morphological parameters was noticed. Fat digestibility registered a statistically significant decrease in the groups fed a high-fat diet with the addition of sprouts. The study shows a new direction in the use of buckwheat sprouts.