Background: There is debate as to whether maternal tobacco use in pregnancy is related to offspring behaviour later on. We tested this association examining multiple aspects of children’s behaviour at age 5 and accounting for parental smoking outside of pregnancy, as well as child and family characteristics. Methods: Data come from a prospective community based birth cohort study (EDEN; n = 1113 families in France followed since pregnancy in 2003-2005 until the child’s 5th birthday). Maternal tobacco use in pregnancy was self-reported. Children’s socio-emotional development (emotional symptoms, conduct problems, symptoms of hyperactivity/inattention, peer relationship problems, prosocial behaviour) was assessed by mothers using the Strengths and Difficulties Questionnaire (SDQ) at age 5 years. Logistic regression analyses controlled for Inverse Probability Weights (IPW) of maternal tobacco use calculated based on study center, children’s characteristics (sex, premature birth, low birth weight, breastfeeding), maternal characteristics (age at the child’s birth, psychological difficulties and alcohol use in pregnancy, post-pregnancy depression, and smoking), paternal smoking in and post-pregnancy, parental educational attainment, family income, parental separation, and maternal negative life events. Results: Maternal smoking in pregnancy only predicted children’s high symptoms of hyperactivity/inattention (sex and study center-adjusted ORs: maternal smoking in the 1st trimester: 1.95, 95%CI: 1.13-3.38; maternal smoking throughout pregnancy: OR = 2.11, 95%CI: 1.36-3.27). In IPW-controlled regression models, only children of mothers who smoked throughout pregnancy had significantly elevated levels of hyperactivity/inattention (OR = 2.20, 95%CI: 1.21-4.00). Conclusions: Maternal tobacco smoking in pregnancy may contribute directly or through epigenetic mechanisms to children’s symptoms of hyperactivity/inattention.