To better understand the role of neuroendocrinological regulation in adolescent mental health, stress reactivity needs to be analyzed through both the autonomic nervous system (ANS) and the hypothalamic-pituitary-adrenal (HPA) axis. Accordingly, this study examined how adolescents' internalizing and externalizing mental health symptoms are associated with their salivary alpha-amylase and cortisol levels, responses, and coordination (symmetry versus asymmetry). We utilized a developmentally salient stress task of mother-adolescent conflict discussion. Eighty 18-20-year-old late adolescents (55% girls) participated in a home laboratory assessment involving a 10-min conflict discussion with their mothers. Five adolescent saliva samples were collected to measure alpha-amylase and cortisol levels before, immediately after, and in 10-min intervals following the conflict discussion, to indicate stress reactivity. Adolescents had reported their internalizing (depression, anxiety, somatization) and externalizing (inattention, hyperactivity, anger control problems) symptoms 1 year earlier as part of a prospective family study. Internalizing symptoms were associated with adolescents' high baseline cortisol levels, but not with cortisol responses or alpha-amylase levels or responses. In contrast, externalizing symptoms were associated with blunted alpha-amylase responses. Neither internalizing nor externalizing symptoms were associated with asymmetry between alpha-amylase and cortisol reactivity. The mother-adolescent conflict discussion was relevant as a stress stimulus to induce neuroendocrinological stress responses in adolescents. The nature of mental health problems was important for stress reactivity, yet, we found no evidence about mental health problems being related to endocrinological asymmetry in adolescents.