It is generally accepted in practical veterinary medicine that cryptosporidiosis invasion of the gastrointestinal tract of calves is a local pathological process and the disease outcome is completely determined by the local etiological factor. Pathomorphological changes in the gastrointestinal tract, detected during the invasion, and metabolic disorders in the body of sick calves cannot occur without changes in the structure of adaptive mechanisms. Therefore, studies of the endocrine organs reaction in acute and chronic forms of the cryptosporidiosis course have been carried out. It has been found that calves during the neonatal period have the acute course of invasion accompanied by severe violations of the most functionally loaded structures of the endocrine organs. This is manifested in the form of increased mechanisms of programmed necrosis, the occurrence of reversible and irreversible degenerative processes, and local hemocirculation disorders. The pathological metamorphosis arising from cryptosporidiosis infection in endocrinocytes led to significant violations of the adaptive systems of the calves’ body and ultimately ended in an unfavorable disease outcome. Pathological changes with a predominance of atrophic, sclerotic, and necrobiotic processes in the chronic course of invasion were manifested in all structures of the studied endocrine organs simultaneously. A prolonged state of structural and functional overstrains of the endocrine organs eventually led to the depletion of adaptive hormone resources. The pluriglandular insufficiency state in the body was crucial in the pathogenesis and outcome of the chronic course of cryptosporidiosis in calves.