Human respiratory system is harbored by a vast array of transient and normal microbial flora. Anumber of pathogenic viruses were diagnosed from samples in different occasions from mild tosevere infections of respiratory tract. Molecular methods were developed for detection of theseviruses during last two decades. Nucleic acid amplification methods were introduced for rapidand accurate diagnosis of pathogenic viruses. Multiplex detection systems were employed toidentify a panel of pathogenic viruses, which requires specialized kits and instruments in somecases. This review summarizes different types of molecular approaches which were developedwith time and applied for the detection of pathogenic viruses associated with infections of therespiratory system.