Objective: To describe the characteristics of pregnant women who accept the influenza vaccine and evaluate the relationship between vaccination and adverse pregnancy outcomes. Methods: Retrospective cohort study of women receiving prenatal care during the 2009-2011 influenza seasons. Vaccination status was ascertained through our perinatal record system and clinic vaccination logs. Pregnancy outcomes included a primary composite of miscarriage, fetal demise, preterm birth (PTB) <37 weeks and neonatal demise. Stratification and logistic regression were used to adjust for potential confounders. Results: Of 3104 eligible pregnant women, 1094 (35%) received the influenza vaccine. Women vaccinated were more likely to be older, obese, primiparae, and have medical complications or a prior PTB. In univariable analyses, flu vaccination was associated with increased adverse composite outcome and PTB. After multivariable adjustments, vaccination was no longer associated with adverse outcomes in women with medical complications but remained associated with adverse outcomes among those without known co-morbidity. Conclusions: Vaccination was associated with an increased adverse composite outcome in pregnant women without identified co-morbidity but not those with co-morbidities. This association is likely due to selection bias, which should be considered in planning of observational studies of the impact of vaccination on pregnancy outcomes. © 2013 Informa UK Ltd. All rights reserved: reproduction in whole or part not permitted.