Psychophysiological responses during affect regulation were examined in 57 children ages 3-9 years, 41 of whom had a parent history of childhood-onset depression (COD). During a structured laboratory task, children were given first a disappointing toy and then a desired toy. Frontal electroencephalogram (EEG) asymmetry, respiratory sinus arrhythmia (RSA), heart period, and heart period variability were measured during resting and task conditions. Affective and self-regulatory behaviors were coded from videotape. In 3-5-year olds, greater relative right frontal activity was associated with withdrawal behavior. High heart period was associated with approach behavior. Compared with children of psychiatrically healthy parents, children of parents with COD exhibited poor heart period recovery after disappointment. For children of parents with COD, greater relative left frontal activity was related to concurrent internalizing and externalizing problems, and low resting RSA was related to internalizing problems. Physiological responses associated with affect regulation may help identify children at risk for depression.