Recently, many cases of mixed invasion by Giardia and ascarids have been registered. Gastrointestinal lesions in patients are often accompanied by dysbiotic changes. The aim was to study the effect of probiotics containing Saccharomyces bouvardias CNCM I-745 in the complex therapy of patients with giardiasis, ascariasis, and mixed invasion. 90 patients with giardiasis, ascariasis and mixed invasion were divided into 3 groups, depending on the type of invasion. Each group was divided into two subgroups, depending on the treatment (basic treatment and treatment with probiotics). When studying the state of the intestinal microbiota, the following changes were detected in all patients before treatment. The content of Bifidobacterium spp., Lactobacillus spp., Enterococcus spp. and the total content of E. coli was reduced. At the same time, there was an increase in the content of Peptostreptococcus spp., Bacteroides spp., E. coli with low enzymatic properties, hemolytic E. coli, opportunistic Enterobacteriaceae spp., Candida spp. and Staphylococcus spp. Under the influence of treatment, the subgroup with probiotics addition to the basic treatment, was more effective for all types of invasions. The use of probiotics containing Saccharomyces bouvardias CNCM I-745 in the complex therapy of patients with mixed invasion of giardiasis and ascariasis increased treatment efficiency following a significant improvement in intestinal microbiota.