During and after pregnancy, it is common for mothers to feel anxious. Children born to mothers with high anxiety are more likely to have behaviour problems. These behaviour problems might be related to brain differences in the amygdala, which is a brain area involved in emotion. We investigated how mothers’ anxiety during and after pregnancy was related to brain function in their children. Mothers with anxiety during pregnancy had children with less functional communication between the amygdala and parietal brain regions. After pregnancy, mothers with anxiety had children with larger amygdalas. These changes in brain function and structure are similar to what is seen in children and adults with anxiety and depression. Therefore, identifying and treating prenatal anxiety will likely help promote healthy outcomes for both mothers and their children.