Respiratory virus infections place a great burden on people all over the world, because of the high morbidity and mortality. Within the outbreaks of severe acute respiratory syndrome (SARS) and the more recent avian H5N1 and H7N9 influenza virus, the patient care providers face an enormous challenge in rapidly diagnosing vial respiratory infections. Molecular diagnostic techniques have a great development during the past decade. These techniques have been necessary diagnostic tools in rapid detection of viral pathogens causing respiratory infections for their high sensitivity and specificity. Several molecular techniques leading by nucleic acid amplification techniques provide decrease in turnaround time and the gold standard for diagnosis of respiratory viruses, which has shifted away from classic diagnostic methods to molecular techniques in most clinical laboratories.