In addition to its antimicrobial protective role, the gut microbiota affects human metabolism and immunity as well as inflammatory and neuro-hormonal responses. Due to its beneficial effects on health even up to the genetic level, it is referred to as a “forgotten organ,” “virtual organ,” or “other brain” (1). The human gut microbiome differs among individuals and usually does not change over time. Its composition is affected by several environmental factors (1-3). Fecal microbiota transplantation (FMT) or bacteriotherapy (health donor stool transplantation) is the instillation of a fecal suspension taken from a healthy donor into the upper or lower gastrointestinal (GI) tract of a patient, with an aim to enrich and normalize his or her gut microbiota. Although the method has been known for centuries, interest in it has significantly grown over the last few decades. The two main reasons are the global epidemic of Clostridioides difficile (CDI) infection and an improved knowledge of the GI microbiome and its involvement in various conditions. It seems that FMT may also transfer host phenotype. Many studies have shown the effectiveness of FMT when used as a therapy for recurrent and refractory CDI. Excellent treatment results were also observed in patients with multiple diseases and in immunosuppressed patients. The success rate was exceptional, up to 90%, in recurrent or refractory CDI (4,5). According to the known clinical evidence, no absolute contraindication for FMT has been encountered (6). Besides the use in CDI patients, the implementation of FMT would probably be expanded by new insights linking gut microbes to the pathophysiology of other intestinal and extraintestinal diseases. Stool donor may be any health individual, such as partner, relative, friend, or genetically unrelated and formerly unknown healthy person. Donors should be tested for various infections and conditions that carry an increased risk of disease transmission (5,6). Regarding stool preparation, a freshly prepared donor stool specimen should be transferred within 6 h after evacuation. Normal saline is mostly used, but water or milk are also viable alternatives. Solid stool is usually diluted in solvent at a ratio of 1:3 or 1:5. The aim is to prolong the duration of the transferred stool in the recipient's gut, so it is important to ensure a high viscosity of the stool suspension. Stool specimen is homogenized and then filtered. A processed specimen is usually instantly infused into the gastrointestinal tract, but it can also be prepared for freezing or for the production of encapsulated preparations (7,8). Mastering the preparation process of frozen stool is crucial for the establishment of a stool bank, which would ensure accessibility without waiting for new donations or their screening. Randomized control trials found no difference between the use of fresh and frozen fecal samples for the treatment of resistant CDI (7-9). Fecal transfer can be performed in several ways. In the colonoscopic method, fecal suspension is infused trough a working channel of colonoscope and installed in the colon ascendens and cecum. In most cases, the volume of the installed stool is about 200-500 mL (6,10). Another method is the application by means of nasojejunal tube. In this case, the volume of fecal suspension is much lower (25-50 mL). Despite all the benefits, long-term outcomes and the potential adverse events (AEs) related to FMT remain the main concerns. AEs are usually divided into two categories: microbiota-related and delivery-related (11). Microbiota-related AEs result from the interaction between transplanted microbiota and the host (fever, bacteremia, allergic reaction, disease exacerbation or relapse, and transmission of unwanted pathogenic organism infection). Delivery-related AEs are a consequence of the modality of infusion (vomiting, aspiration pneumonia, post-procedural abdominal pain, nausea, proctalgia or anorectal discomfort, bowel perforations, and sore throat) (11).