BackgroundHeavy alcohol use during pregnancy can cause considerable developmental problems for children, but effects of light‐moderate drinking are uncertain. This study examined possible effects of moderate drinking in pregnancy on children's conduct problems using a Mendelian randomisation design to improve causal inference.MethodsA prospective cohort study (ALSPAC) followed children from their mother's pregnancy to age 13 years. Analyses were based on 3,544 children whose mothers self‐reported either not drinking alcohol during pregnancy or drinking up to six units per week without binge drinking. Children's conduct problem trajectories were classified as low risk, childhood‐limited, adolescence‐onset or early‐onset‐persistent, using six repeated measures of the Strengths and Difficulties Questionnaire between ages 4–13 years. Variants of alcohol‐metabolising genes in children were used to create an instrumental variable for Mendelian randomisation analysis.ResultsChildren's genotype scores were associated with early‐onset‐persistent conduct problems (OR = 1.29, 95% CI = 1.04–1.60, p = .020) if mothers drank moderately in pregnancy, but not if mothers abstained from drinking (OR = 0.94, CI = 0.72–1.25, p = .688). Children's genotype scores did not predict childhood‐limited or adolescence‐onset conduct problems.ConclusionsThis quasi‐experimental study suggests that moderate alcohol drinking in pregnancy contributes to increased risk for children's early‐onset‐persistent conduct problems, but not childhood‐limited or adolescence‐onset conduct problems.