Atypical pneumonia was first described in 1938, and over time, Mycoplasma, Legionella, and Chlamydophila were the agents commonly linked with community-associated atypical pneumonia. However, as technology has improved, so has our understanding of this clinical entity. It is now known that there are many agents linked with atypical pneumonia in the community, and many of these agents are also major causes of healthcare-associated pneumonia. This article discusses the history, epidemiology, and pathogenesis of infection; control of infection; clinical findings; diagnosis; and, where applicable, treatment of the agents of healthcare-associated atypical pneumonia. Bacterial agents include Legionella species, Mycoplasma pneumoniae, Chlamydophila species, and Coxiella burnetii. Although there are over 100 viruses that can cause respiratory tract infections, only a fraction of those have been defined in the context of healthcare-associated atypical pneumonia: adenovirus and human bocavirus (HBoV); rhinovirus; human coronaviruses (HCoV), including HCoV 229E, HCoV OC43, HCoV NL63, HCoV HKU1; members of the paramyxoviridae (parainfluenza viruses, human metapneumovirus, and respiratory syncytial virus); hantavirus; influenza; and severe acute respiratory syndrome (SARS) Co-V. Our knowledge about healthcare-associated atypical pneumonia will continue to evolve as newer pathogens are identified and as newer diagnostic modalities such as multiplex polymerase chain reaction are introduced.