Fecal microbiota transplantation (FMT) is a treatment modality that involves the process of transplanting fecal matter obtained from a selected donor to a recipient in order to restore the microbial homeostasis in the intestine. Although the utilization of fecal matter to treat diseased individuals can be traced to the 4th century, China, it was not until the end of the 20th century that Western countries began to study the potential role of FMT. Since then, there has been a growing interest in the scientific community to understand the composition and the function of the human microbiota. In addition, there has also been a great deal of interest in how to manipulate the microbiota and to understand the relationship between various disease conditions and the perturbated microbial community. In contrast to antibiotics and immunomodulators, FMT seems to be an excellent therapy option for several gastrointestinal diseases, as it is a restorative treatment modality and not destructive or suppressive. The mechanism of action of FMT is not fully understood, however, its effectiveness is thought to be attributable to the recovery of the microbiota from dysbiosis to eubiosis. To date, the only formally approved indication for FMT is Clostridioides difficile infection (CDI), in addition, the reported efficacy rates have been very high. The findings on employing FMT for treating inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) are not as straightforward, possibly due to the limited large-scale RCTs, the heterogenous nature of the disease, the various phenotypic presentations and the still unknown factors associated to the transplanted microbiota. Nevertheless, FMT seems to have a role in both IBD and IBS management and could be incorporated as an adjunctive therapy to combat not only dysbiosis and related pathology but also the additional pathogenetic mechanisms that usually underlie these multifactorial-related conditions.