OBJECTIVES: To investigate whether patient reported outcomes could detect differences between H1N1 and seasonal influenza vaccinations on adverse events over a 26 week follow up period. METHODS: In this evaluation, PROBE methodology consisting of a web-based system supplemented by telephone reporting was used to collect naturalistic data from people who had received an influenza vaccination during 2009-2010 season. People were recruited through media advertising and awareness campaigns in public places and work (West of Scotland).  Data collection on day of immunisation, after 3 days, 8 days, 6 weeks, 12 weeks and 26 weeks.  Data included age, sex, presence or absence of chronic illness, flu vaccination history, any side effects following vaccination including the duration and action taken. RESULTS: A total of 1103 vaccine recipients including 134 young children (<5 years) participated; 694 (63%) received H1N1 vaccine only, 135 (12%) seasonal only, 224 (20%) both H1N1 and seasonal vaccines and 50 (5%) received H1N1 or seasonal vaccine with a non-influenza vaccine (e.g. travel or pneumococcal). Overall, 70% of respondents reported experiencing a side effect after vaccination – this includes pain/discomfort at the injection site and any other side effects.  Of the 964 recipients of an H1N1 vaccine, significantly more (511, 74%) experienced a side effect compared with those who received only the seasonal flu vaccine (45%, χ2-test p <0.001). Multivariate regression analysis revealed that female sex and the H1N1 vaccination were more likely to report any side effect (OR 2.10, p<0.001 and OR 4.47, p<0.001 respectively) and age > 70 less likely to report (OR 0.29, p<0.001). CONCLUSIONS: People receiving the H1N1 vaccination were more likely to experience side effects than seasonal influenza vaccination alone. This evaluation shows that the PROBE methodology quickly and simply captured patient reported outcome information in a vaccinated population including children.