In this study, parameters indicative of adrenocortical and sympathoadrenal function were determined in foals (n = 43). Foals were assigned to the following groups: Healthy home (n =10, born and kept at their home stud), Healthy clinic (n =11, born to mares hospitalized for surveillance of foaling), Colostrum (n = 4, received colostrum by bottle or nasogastric tube, no signs of disease), Failure of passive transfer (n = 8, received hyperimmune serum, no signs of disease), Sepsis (n = 5) and Prematurity (n = 5). Saliva for cortisol analysis was collected four times daily and heart rate for analysis of heart rate variability (HRV) was recorded once daily during the first 5 days of life. On day 1, cortisol concentration was elevated (p < 0.001), reflecting the demands of neonatal adaptation, but did not differ among groups. On days 2-5, cortisol concentration in premature foals, was higher (p < 0.05) than in all other groups, indicating adrenal maturation. Cortisol concentration did not differ between foals that required frequent examination and treatment and healthy foals. This indicates that handling was not perceived as stressful. In none of the foal groups, salivary cortisol concentration was reduced compared to healthy foals. Heart rate in septic foals was elevated throughout the observation period (p < 0.05) but this was not associated with a poor outcome. Heart rate was not influenced by handling of the foals. The HRV did not differ among groups and sepsis was not associated with decreased HRV, at least if treatment is initiated early. In conclusion, adrenocortical and sympathoadrenal function of foals was neither consistently activated nor depressed by neonatal sepsis. Increased cortisol release in premature foals in the first days of life may reflect maturational processes that occur already shortly before birth in term foals.