Atypical pneumonia can be caused by a variety of organisms such as Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella pneumophilla, Coxiella burnetii, SARS, RSV and adenovirus. It can be associated with high morbidity and mortality rates.Conventional diagnostic methods as direct antigen detection, culture and serology have several drawbacks. Culture is time consuming, difficult, and insensitive. Serology requires paired sera 2-4 weeks apart so it provides retrospective diagnosis and serological results are difficult to interpret.Molecular methods can provide rapid and accurate diagnosis of atypical pneumonia and multiplex PCR assays are available. Molecular applications are of great value in rapid identification of newly emerging pathogens, epidemiology investigation to determine the source of infection in outbreaks and antimicrobial resistance.