OBJECTIVES: In April 2009, WHO announced the emergence of Influenza A (H1N1) and a phase 6 pandemic was declared a few months later. Vaccination was identified as an effective measure in order to eliminate the pandemic and ensure public health. The aim of the present study was to investigate the factors affecting parents’ decision to vaccinate their children. METHODS: A telephone survey was conducted in a random sample of 12,639 households stratified by geographical area using a strictly structured questionnaire designed for the purpose of the study. The survey lasted from October 2009 to January 2010. A logistic regression analysis was conducted in order to identify the factors that influence parents’ decision to vaccinate their children. The Hosmer–Lemeshow criterion was used to check the model’s goodness of fit. RESULTS: A total of 3585 households were eligible and were included in the analysis. Education, income, concern about H1N1 and trust to the CDC were statistically significant. According to the analysis the higher the levels of education (OR 0.64) and income (OR 0.80) of the parents the lower the probability to vaccinate their children. However, the interaction term between education and income showed a positive relationship between these and the dependent variable. The greater the concern about H1N1 and the trust to the CDC the higher the probability for the parents to vaccinate their children. The Hosmer–Lemeshow goodness of fit test statistic was 0.52 suggesting satisfactory fit of the model. CONCLUSIONS: Based on our results concerns about the H1N1 and trust on the CDC were influencing positively the decision for vaccination. The negative relationship between education and income and parents’ decision for vaccination was interesting and need further investigation. Results can explain the low vaccination rates against H1N1 in Greece and can be used by policy makers to improve future vaccination campaigns.