Surgical pathology results can play a crucial role in the management of immunocompromised patients. Here we highlight factors that differ between immunocompromised and immunocompetent hosts, such as variation in inflammatory response. Conditions that are covered include drug reactions, disease within solid organ allografts, immune reconstitution inflammatory syndrome, specific immunodeficiency syndromes, neoplasms related to viral infections, and viral, bacterial, fungal, and parasitic infections. Special techniques including immunohistochemistry, in situ hybridization and molecular detection of pathogen nucleic acid from formalin-fixed, paraffin-embedded tissue are discussed.