Objective: To examine in a nonclinical sample of preadolescents the possibility that somatic and cognitive-affective depressive symptoms are differentially related with the autonomic nervous system (ANS) and the hypothalamic-pituitary-adrenal (HPA) axis. Depression is a well-known risk factor for cardiovascular disease and mortality. Dysregulation of the ANS and the HPA axis have been proposed as underlying mechanisms. Several studies suggest that only a subset of the depression symptoms account for associations with cardiovascular prognosis. Methods: Self-reported somatic and cognitive-affective depressive symptoms were examined in relationship to heart rate variability (HRV), spontaneous baroreflex sensitivity (BRS), and the cortisol awakening response (CAR) in 2049 preadolescents (mean age = 11.1 years; 50.7% = girls) from the Tracking Adolescents' Individual Lives Survey (TRAILS). Results: Physiological measurements were not associated with the overall measure of depressive symptoms. Somatic depressive symptoms were negatively related to HRV and BRS, and positively to the CAR; cognitive-affective depressive symptoms were positively related to HRV and BRS, and negatively to the CAR. Associations with the CAR pertained to boys only. Conclusions: Somatic and cognitive-affective depressive symptoms differ in their association with both cardiac autonomic and HPA axis function in preadolescents. Particularly, somatic depression symptoms may mark cardiac risk.