Background Viral acute respiratory infections (ARI), including respiratory syncytial virus (RSV) and human rhinovirus (HRV), induce acute wheezing episodes in young children. This study aimed to determine the association of wheezing with respiratory viruses, demographic and clinical characteristics in young children. Methods A prospective viral surveillance study in children less than two years, admitted with fever and/or respiratory symptoms in Amman, Jordan, 2010-2013. Demographic and clinical characteristics were collected through parent interviews and medical chart abstraction. Nasal/throat swabs were collected and tested by qRT-PCR. Multivariable logistic regression was fit to assess the association between wheezing and a-priori selected predictors of interest. Results Of 3168 children enrolled, 1757 (55%) were wheezing-positive, who were older, more likely to have a respiratory virus, underlying medical conditions, personal history of reactive airway disease (RAD), and a family history of asthma, compared to wheezing-negative children. Older age, personal history of RAD, family history of asthma, RSV and HMPV were associated with higher odds of wheezing in an adjusted regression model. Conclusion In young children, RSV and HMPV were associated with higher odds of wheezing. Longitudinal studies are needed to evaluate the association between early childhood viral ARI and recurrent wheezing later in childhood, to guide preventive interventions.