Patients in intensive care unit often lose a considerable fraction of their gut microbiome due to exposure of broad-spectrum antibiotics and other reasons. Dysbiosis often results in prolonged diarrhea and increase occurrence of multi-drug resistant pathogens in the colon with clinical consequences not yet well understood. Restoring the microbioma by faecal microbial transplantation (FMT) is a plausible therapeutic possibility, so far only documented in case reports and case series using very heterogeneous methodologies. Before FMT in critically ill can be tested in randomised controlled trials, there is a burning need to describe a standardized operating procedure (SOP) of the whole process, respecting the specifics of critically ill population, such as the risk of disrubted intestinal barrier and time critical nature of the procedure. We describe the SOP that has been developed for experimental use in critically ill patients by a multidisciplinary team of intensivists, gastroenterologist and microbiologist based on feedback from regulatory authority (State Institue of Drug Control of the Czech Republic). The hallmarks of these SOPs are multi-donor freshly frozen transplantate quaranteeded for 3 months consisting of 7 aliqutes from 7 unrelated healthy donors, and administered by rectal tube. In this paper we discuss the rationale for this SOP and the process of its development in details and release the full proposed SOP is in the form of online appendix.