Since viruses are the main cause of asthma, especially in children under 5 years old, and they are also involved in the etiology of bronchiolitis, we decided to survey the prevalence of three main viruses; respiratory syncytial virus (RSV), human rhinovirus (HRV), and human metapneumovirus (hMPV), in children with acute wheezing in our hospital. We hope that this study will provide a baseline for future studies about the clinical importance of particular viral prevalence. Background: Viruses are known to cause the majority of acute respiratory infections. A great deal of evidence indicates that the etiology of most cases of wheezing in children, like asthma or bronchiolitis, is also linked to such respiratory infections. Objectives: We assessed the prevalence of three common viruses including; respiratory syncytial virus (RSV), human rhinovirus (HRV), and human metapneumovirus (hMPV), in children with acute wheezing. Patients and Methods: Ninety six wheezy children, 48 males (50%) and 48 females (50%) under the age of 5 years, were enrolled in the study. All patients visited as outpatients or inpatients when referred to the Mofid Children's Hospital, in Tehran, from September 2009 to March 2010. A nasopharyngeal sample was taken from each child's nostril and the three viruses were detected by a molecular polymerase chain reaction method (PCR). Results: Out of 96 patients, 63 cases (64.8%) had a positive PCR test for at least one virus. Prevalence of each virus including RSV, HRV and hMPV alone or in combination were 44 (45.8%), 13 (13.5%) and 6 (6.3%), respectively. There were no significant relationships between; age, prematurity, fever, respiratory distress and the existence of any kind of virus in the nasopharynx. Conclusions: Our study revealed that the prevalence of these three viruses in the nasopharyngeal secretions of children suffering from acute wheezing was similar to other studies. The results of this study concluded; PCR assay is a widely available and rapid method to detect the viral etiology which induces wheezing in children in Iran, and the study also provides a baseline for future studies about the clinical importance of this relationship.