Viral Respiratory Tract Infections (RTIS) are considered to be a major public health problem due to their worldwide occurrence, ease of spread and being one of the major causes of morbidity and mortality among adult and children under the age of five. They are responsible for the economic burden on the society. Therefore, detection of these viruses is essential for a better patient management and reduction of costs. The current study is the first in the Sultante of Oman to investigate 13 respiratory viruses and their role in RTIs. The objectives of the study were to estimate the rate of respiratory viruses in children <5-years-old with RTIs and to evaluate the role of these viruses in respiratory illness. Moreover, to compare the sensitivity and the specificity of the molecular method to the direct immunofluorescence assay (DFA) in detection of these viruses, to identify the seasonal distribution of respiratory viruses and to recognize the potential risk factors that might be associated with RTIs. In order to achieve those objectives 259 nasopharyngeal aspirates (NPAs) were collected from young children and infants < 5 years old admitted to SQUH with a diagnosis of RTIs. DFA was routinely used for the detection of RSVs, Flu A and B, PIVs 1, 2 or 3 and adenovirus. While the molecular method detected additional viruses; including coronaviruses, human rhinoviruses and hMPV using a new multiplex RT-PCR format. Human bocavirus was detected separately in a single conventional PCR format. Among the 259 tested NPA specimens, 130 (50.2%) were positive for at least one virus. Out of the 259 specimens, RSV was found to be the most predominant pathogen involved in the respiratory infection with a rate 21.6% followed by adenovirus then PIVs and Flu A with a rate of 10.4%, 7.7% and 7.3% respectively. The molecular method used successfully detected other viruses not routinely detected by DFA such as rhinovirus A/B, bocavirus, hPMV and coronavirus 229E/NL63 with rates of 6.95%, 3.5%, 1.2% and 0.8% respectively. The detected viruses were found to be associated with lower respiratory infections including bronchiolitis and pneumonia in which RSV was the leading cause of these infections. Twenty three co-infections cases were reported with a rate of 17.7%. Among 33 NPA control samples collected from individuals without respiratory symptoms, 6 were positive for respiratory viruses. The seasonal distribution of some RVs was investigated in this study. The overall sensitivity and the specificity of the new method compared to the DFA for detection of common RVs were 28.6% and 75.0% respectively with no significant disagreement between the two methods (McNemer's x =0.17< 3.84, so p = 0.68 > 0.05) and 64 % agreement (kappa test =0.64, good agreement). According to these findings the PCR method can be used for detection of the common RVs as well as the additional respiratory viruses that are difficult to be detected by DFA provided that the specimens should be processed within 1-3 hours after collection.