Background: Secondary immunodeficiency in recipients after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the pediatric practice is often accompanied by bacterial and viral infections of the gastrointestinal tract (GIT), resistant to conventional therapy. Fecal microbiota transplantation (FMT) promotes intestinal recolonization and eradication of gastrointestinal symptoms. Clinical case description: A 2.5-year-old patient underwent allo-HSCT from a haploidentical related donor (father) as a part of the treatment of acute myeloid leukemia. A month after the last procedure, diarrhea (up to 10 times a day) and abdominal pain appeared. The astrovirus RNA and Clostridium difficile toxin A were detected in the feces. The FMT was prescribed. After two FMT procedures, the intestinal syndrome leveled out, and the tests for the astrovirus RNA and clostridial toxins were negative. The content of cholic and, in particular, deoxycholic acids, as well as their conjugates with glycine and taurine, in the feces increased; the acetic acid content increased with a simultaneous decrease in the level of propionic acid, which indicates the restoration of the intestinal microbiotas functional potential. Conclusion: FMT contributes to the restoration of the normal intestinal microflora, the elimination of clostridial toxins, enteroinvasive E. coli and astrovirus infection in allo-HSCT recipients, as evidenced by the indicators of the intestinal microbiota activity, and can be used in allo-HSCT recipients with infections refractory to conventional therapy.