Wheezing phenotypes may not be stable, and phenotype transitions may occur over time. This study investigates the natural course of episodic viral wheezing (EVW) and identifies the risk factors that predict persistence of wheezing through short-term follow-up. The medical records of children <3 years of age at hospital admission and classified as having EVW were retrospectively screened by two pediatric allergists. A total of 236 children were classified as having EVW between January 2010 and February 2011. The median follow-up period was 19.5 months. At the end of follow-up, wheezing persisted in 145 patients (61.4%) and changed to multiple-trigger wheeze in 37 patients (15.7%). Factors associated with persistent wheeze were age at initial wheezing <24 months, anti-inflammatory treatment at the time of diagnosis, history of severe episodic wheeze in the previous year, wheezing requiring systemic steroids in the previous year, frequent episodic wheeze, parental asthma, and a positive modified asthma predictive index (mAPI) for major criteria (each, p <0.05). The logistic regression analysis revealed three independent risk factors: anti-inflammatory treatment at the time of diagnosis (p <0.03), history of severe episodic wheeze in the previous year (p <0.02), and a positive mAPI for major criteria (p <0.02). The initial wheezing phenotype may vary over time. History of severe episodic wheeze in the previous year, anti-inflammatory treatment at the time of diagnosis, and a positive mAPI for major criteria predicts persistent wheeze at short-term follow-up.