Annual influenza vaccination is recommended for healthcare workers, but many do not follow the recommendation. The objective of this study was to investigate the factors associated with seasonal influenza vaccination in the 2011– 2012 season. We carried out an anonymous web survey of Spanish primary healthcare workers in 2012. Information on vaccination, and knowledge and attitudes about the influenza vaccine was collected. Workers with medical conditions that contraindicated vaccination and those with high risk conditions were excluded. Multivariate analysis was performed using unconditional logistic regression. We included 1,749 workers. The overall vaccination coverage was 50.7% and was higher in workers aged ≥ 55 years (55.7%), males (57.4%) and paediatricians (63.1%). Factors associated with vaccination were concern about infection at work (aOR 4.93; 95% CI 3.72–6.53), considering that vaccination of heathcare workers is important (aOR 2.62; 95%CI 1.83–3.75) and that vaccination is effective in preventing influenza and its complications (aOR 2.40; 95% CI 1.56–3.67). No association was found between vaccination and knowledge of influenza or the vaccine characteristics. Educational programs should aim to remove the misconceptions and attitudes that limit compliance with recommendations about influenza vaccination in primary healthcare workers rather than only increasing knowledge about influenza and the characteristics of the vaccine.