Infections are relevant complications that cause morbidity in solid organ transplantation and autoimmune diseases. Infection represents a leading single cause of death in these patients. Identification of patients at risk for development of infections and specific intervention to decrease infection risk might lead to better outcomes, though one needs first to evaluate the presence of risk factors for infection. Underlying disease itself, activity of the disease, presence of co-morbidities, transplantation procedures along with immunosuppressive and immunomodulatory therapies may be associated with an increased risk of infections. Among host factors, there are no reliable immunological markers to predict infections. Immune monitoring (assessment of immunocompetence) to estimate the risk of infection has so far not been performed routinely, with the only exception of neutrophil counts, tuberculin skin testing and serological evaluation of donor and recipients of transplants for anticytomegalovirus IgG antibodies. However, alterations of specific and non specific humoral and cellular immunity may be associated with a higher risk of infection among immunosuppressed patients. We review studies that have been designed to assess immune monitoring for prediction of infections in patients with selected solid organ transplantations and systemic autoimmune diseases.