Objectives: Traditionally, influenza is not considered to be a serious disease in healthy children. However, for vulnerable populations, such as young children and those with chronic medical conditions, influenza can lead to serious complications and even death. This study aimed to assess vaccination coverage among Spanish children under 16 years of age in 2006, and to describe the factors associated with vaccination. Study design: Cross-sectional survey. Methods: In total, 8851 records of children included in the Spanish National Health Survey for 2006 were analysed. The reply ('yes' or 'no') to the question: 'Did you have a flu shot in the latest campaign?' was used as a dependent variable. Influenza vaccine coverage was calculated as the percentage of individuals aged 6 months to 16 years whose parents reported that they had been vaccinated against influenza in the most recent campaign. The influence of sociodemographic variables on vaccination and the presence of associated chronic diseases (asthma and/or diabetes) were also analysed. Results: Vaccination coverage among Spanish children in 2006 was 6.82%: 19.43% in children with associated conditions (asthma and/or diabetes), and 5.81% in healthy children. The only factor significantly associated with influenza vaccination in children with associated conditions was household income; children with a lower household monthly income were more likely to have been vaccinated against influenza than children with a higher household monthly income (odds ratio 1.96). In children for whom vaccination is not indicated, the probability of being vaccinated against influenza was greater in those whose parents were not university graduates. Conclusion: Influenza vaccination coverage in Spanish children is low. Socio-economic inequalities continue to be a factor at the time of vaccination. (C) 2009 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.