Background The primary aim of this study was to examine differences in physiological reactivity (measured via pupillometry) to emotional stimuli between children of depressed versus nondepressed mothers. A second goal was to examine differences in pupil dilation to emotional stimuli between children of anxious versus nonanxious mothers. Method Participants included 117 mother–child pairs drawn from the community. Children were between the ages of 8 and 14. Pupil dilation was assessed using an eye‐tracker while participants viewed angry, happy, or sad faces. Results Children of mothers with a history of major depression (MDD) exhibited increased pupil dilation to sad, but not happy or angry, faces compared with children of nondepressed mothers. Second, we found that children of anxious mothers exhibited increased pupil dilation to angry, but not happy or sad, faces compared to youth of nonanxious mothers. Conclusions The current findings add to the growing body of research suggesting that differences in physiological reactivity to depression‐ and anxiety‐relevant cues may represent an important mechanism in the intergenerational transmission of MDD and anxiety.