Immunodeficiency syndromes can either be congenital due to a variety of inherited defects or secondary due to an underlying illness or iatrogenic immunosuppression related to chemotherapy, solid organ, or bone marrow transplantation. Irrespective of the cause, immunosuppressed patients have an increased susceptibility to developing infections, which are a significant cause of morbidity and mortality. In this article, we focus on abdominal infections in children who have iatrogenic immunosuppression related to chemotherapy, bone marrow, or solid organ transplant. The development of infection in this population of patients can be related to compromised mechanical barriers, neutrophil dysfunction, impaired cell-mediated as well as humoral immunities, and splenic dysfunction. The absolute granulocyte count is the most important determinant of susceptibility to bacterial and fungal pathogens in these children, whose risk of infection increases as a function of both degree and duration of neutropenia. Infections in the pediatric cancer patient, hematopoietic stem cell, or solid organ transplant recipient can be classified by classic time increments. Bacteria are isolated in the majority of cases of early neutropenia, whereas fungal pathogens typically cause infection in those with severe or prolonged neutropenic states. This dedicated article not only depicts the imaging findings of entities such as neutropenic colitis, infectious enterocolitis, and fungal infections that occur in children with iatrogenic immunosuppression from antineoplastic therapy as well as bone marrow and solid organ transplantation but discusses the pathophysiology leading to their development. Physician awareness of the types of infectious complications in this population, the time frame in which they classically occur, and the use of appropriate criteria to direct imaging can lead to earlier detection thereby affording patients the opportunity for prompt intervention and subsequently improved quality of life.