Introduction Prior studies found associations between respiratory syncytial virus (RSV) infection, wheezing, and asthma. The present study aimed to examine the risk of wheezing after RSV, by the history of wheezing. Methods We included 39 children hospitalized for RSV infection (cases) and 23 children hospitalized for nonrespiratory tract infection reasons (controls) and followed the children prospectively with regular standardized telephone interviews until 18 months, and again 5 years after inclusion. The risk of wheeze was estimated by odds ratios (OR), comparing children hospitalized for RSV with children hospitalized for other reasons and stratified by wheezing history. Results Eighteen months after hospitalization for RSV, the adjusted OR of wheezing was 3.16 (95% confidence interval: 0.75–13.3). The effect of hospitalization for RSV on the risk of wheeze was significantly present among children who did not wheeze already before inclusion (adjusted OR: 11.83; 95% confidence interval: 1.12–124.9), while the adjusted OR of wheeze was 0.95 (95% confidence interval: 0.10–9.00) among children who wheezed already before inclusion. The adjusted OR of wheeze after hospitalization for RSV among children who did not wheeze before inclusion was 8.50 (95% confidence interval: 0.79–91.6) 5 years after inclusion. Conclusion We conclude that the effect of severe RSV infection requiring hospitalization differs according to the history of wheezing, and wanes with time. We recommend that future studies on severe RSV infection and the risk of subsequent wheeze and asthma include information on prior wheeze and asthma.