The current cross-sectional study investigated basal and stress-challenged hypothalamic-pituitary-adrenocortical (HPA) system function in 102 five-year old kindergarten children (59 boys, 43 girls) who had been assessed by a comprehensive psychological and behavioral test battery. Baseline HPA system activity was significantly increased in girls when compared to boys (p<0.001). Furthermore, basal HPA system activity predicted a high hormonal release during stress with--again--girls showing higher hormonal responses than boys (p<0.01). Importantly, increased HPA system activity (baseline and stress-challenged) was significantly associated with hyperactivity/impulsivity and emotional problems in boys and with positive emotions in girls (p<0.05). These results suggest an occurrence of neurobiological alterations early in development. The observed neurobiological changes are gender specific already at the age of 5 years. Prospective long-term follow up of the identified subjects with HPA axis alterations will clarify if these markers are predictive for the onset of psychiatric disorders.