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Patients with immunocompromised states are increasing in the world not only because of HIV infection but also as a result of better therapies in solid organ transplantation, stem cell transplantation, and leukemia. All these patients are at similar risk of gastrointestinal infections, and the subsequent morbidity and mortality from these infections makes it important to recognize the net state of immunosuppression of each person infected.This review evaluates emerging pathogens, new diagnostic tools and guidelines, and the latest therapies published in the last 12 months in HIV and solid organ transplantation. The echinocandins provide a new therapy for Candida esophagitis, whereas Mycobacterium avium complex therapy may be discontinued with immune reconstitution in patients with HIV. The emergence of antimicrobial-resistant bacteria and viruses is a new threat to managing these infections, especially in poorer countries. Also, several community viruses such as adenovirus were shown to cause significant morbidity to immunocompromised patients. Lastly, the interaction among immunosuppressive medications, diarrhea, and rejection makes an important argument for evaluating patients for infection before adjusting medications.The immunocompromised host is rapidly increasing in the world, resulting in exposures to new pathogenic organisms that cause gastrointestinal infections. New diagnostic tests and better antimicrobial therapy are improving outcomes in patients with access to health care. Unfortunately, these challenges are increasing daily with the development of multidrug-resistant bacteria and viruses that do not respond to standard therapies. The most important factor in overcoming these infections is restoration of the immune system, either by using antiretroviral therapy or decreasing immunosuppression.