Gastrointestinal tract diseases in dogs retain a leading position among other pathologies. At the same time, gastrointestinal parasites are among the most common pathogenic agents in dogs around the world and make a significant contribution to the development of severe gastroenteritis. Giardia sp. is a common cause of acute gastroenteritis in many animal species around the world. Proven participation of Giardia sp. in the development of chronic gastrointestinal disorders, leading to malabsorption and developmental delay in young animals, and, as a result, a decrease in resistance and an increase in susceptibility to reinvasion by giardia and various infections. In this regard, it seems relevant to study the pathogenetic features of the effect of protozoa on the mucous membrane of the small intestine of dogs for the development and improvement of therapeutic regimens. In our work, the therapy of giardiasis in domestic dogs with Drontal plus reinvasion for 6 months was not observed. When treating dogs with giardiasis and cystoisosporosis, the main antiprotozoal drug (Drontal for giardiasis or Stop-Coccid for cystoisosporosis) + antibiotic Cobactan + Probiotic Pro-Colin + vitamin B complex (Milgamma), the dogs were restored 100% on the 30th day after the end of treatment. During long-term follow-up of patients with clinical manifestations of gastrointestinal tract malfunction (a change in the consistency of feces towards softening, refusal to feed, and vomiting) with the use of a prebiotic was not observed.