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Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an effective method to treat malignancy and some solid tumors which may be accompanied by life-threatening immune and infectious complications refractory to standard immunosuppressive and antibacterial therapy. According to literature data, fecal microbiota transplantation (FMT) may be applied to restore functional activity of microbiota and to overcome antibiotic resistance. Two clinical cases of FMT in critical ill patients who had developed acute graft-versus-host disease (aGvHD) of intestine after allo-HSCT are presented in the article. The aim of the study was to assess FMT efficiency and safety in immunocompromised critically ill patients. Results. Following FMT, a complete regress of aGvHD signs as well as reduction of systemic infectious process were registered, due to probable modulation of the immune response. In one patient, elimination from respiratory ways of carbapenemase-producing Klebsiella pneumoniae positive for NDM- and OXA-48- producing was noted, like as elimination of Pseudomonas aeruginosa synthesizing KRS-type carbapenemase. Conclusions. FMT may be considered an alternative approach to intestinal aGvHD treatment in critically ill patients after allo-HSCT.