We studied the effectiveness of the AS03-adjuvanted monovalent vaccine (Pandemrix(®)) for the prevention of severe pandemic influenza A(H1N1)pdm09 in children, in 2009. All children hospitalized for influenza-like illness in Stockholm County during the peak of the pandemic were included. We compared the frequency of vaccinated children between influenza A(H1N1)pdm09 PCR positive cases and PCR negative controls in a retrospective case-control study. 95 cases and 177 controls were identified. About half of the children in both groups were between 6 months and 2 years of age. Only 1/95 (1%) cases had been vaccinated more than 14 days prior to admission, compared to 23/177 controls (13%), corresponding to a vaccine effectiveness, adjusted for co-morbid conditions, of 91% (95% confidence interval [CI] 30-99). In contrast, the risk for being a case was significantly higher among children vaccinated between 1 and 14 days prior to hospitalization, than among those who were non-vaccinated 13/95 vs. 7/177 (OR 3.6, 95% CI 1.4-9.5). We conclude that a single dose of adjuvanted vaccine was highly protective against hospitalization for influenza A(H1N1)pdm09 in children 6 month to 17 years. The reason for the increased rate of hospitalizations with confirmed influenza in children just following immunization is unclear and should be studied further.