Organ transplantation is considered the main therapeutic approach for the treatment of a wide variety of end-stage diseases. Transplantation success rate is dependent on the type of engrafted organs, as well as on the different kinetics of inflammation and immune-mediated responses towards donor antigens during the process. Several environmental factors seem to influence solid organ transplantation (SOT) outcomes, especially the composition of the donor’s gut microbiota. Gut microbiota acts as a critical player in the process of maturation and modeling of immune responses, modulating not only local but also systemic immune responses. Emerging evidence from animal and human studies have shown that end-stage disease followed by SOT (e.g. kidney, small bowel, liver, lung, and heart transplantation) can significantly change gut microbial populations. These changes result in a wide range of outcomes, including intense alloimmune responses, characterized by high frequency of Th1 and Th17 CD4⁺ T cells. Even though there has been significant progress in the field, it is still important to better characterize the changes in the gut microbiota populations and the mechanisms by which the host immune responses are influenced, which could contribute to additional intervention strategies aimed at improving graft and patient survival. Therefore, this review explores the positive and the negative effects of the gut microbiota in SOT.