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Annual recommendations on influenza seasonal vaccination include community pharmacists, who have low vaccination coverage. The aim of this study was to investigate the relationship between influenza vaccination in community pharmacists and their knowledge of and attitudes to vaccination. An online cross-sectional survey of community pharmacists in Catalonia, Spain, was conducted between September and November 2014. Sociodemographic, professional and clinical variables, the history of influenza vaccination and knowledge of and attitudes to influenza and seasonal influenza vaccination were collected. The survey response rate was 7.33% (506 out of 6906); responses from 463 community pharmacists were included in the final analyses. Analyses were performed using multivariable logistic regression models and stepwise backward selection method for variable selection. The influenza vaccination coverage in season 2013–2014 was 25.1%. There was an association between vaccination and correct knowledge of the virus responsible for epidemics (adjusted Odds Ratio (aOR) = 1.74; 95% CI 1.03–2.95), recommending vaccination in the postpartum (aOR = 3.63; 95% CI 2.01–6.55) and concern about infecting their clients (aOR = 5.27; 95% CI 1.88–14.76). In conclusion, community pharmacists have a very low influenza vaccination coverage, are not very willing to recommend vaccination to all their customers but they are concerned about infecting their clients. Full article