This article substantiates a differentiated approach to the management of children with detectable commensal protists (Blastocystis spp., Dientamoeba fragilis, Entamoeba coli, Endolimax nana), based on a retrospective analysis of 325 outpatient records of patients aged 1–17 years. The relevance of the study stems from the lack of standardised diagnostic algorithms, which leads either to unwarranted antiparasitic therapy in asymptomatic carriers or to a watchful-waiting approach in symptomatic individuals.Blastocystis spp. was identified in 54.8% of cases, with mixed infections observed in 31.4% (more frequently in girls, with age peaks at 7–10 and 15–17 years). Gastrointestinal complaints were reported in 76.9% (abdominal pain predominantly associated with Blastocystis spp., and dyspepsia and perianal pruritus with D. fragilis), allergic manifestations in 43.7%, and neurological symptoms in 28.9%. Eosinophilia >8% was recorded in 37.2% (most commonly in D. fragilis – 49.3% – and in mixed infections – 58.8%), dysbiosis in 68.3%, and chronic comorbidities in 71.4%. Prior unjustified therapy (38.5%) proved ineffective in 91.4% of cases, was accompanied by progression of dysbiosis in 71.6%, and by recurrence in 73.8%.A five-criteria algorithm is proposed, encompassing: presence of symptoms, eosinophil count, pathogen species, status of the intestinal microbiota, and concomitant diseases. It is concluded that antiparasitic agents are indicated not merely on the basis of protist detection, but rather when clinical symptoms, eosinophilia, and microbiota disturbances coexist. Correction of dysbiosis and management of underlying pathology are mandatory in all clinically significant cases.