Background This study investigated basal and stress-induced hypothalamic-pituitary-adrenal (HPA)–axis alterations in dissociative disorders (DDs). Methods Forty-six subjects with DD without lifetime post-traumatic stress disorder (PTSD), 35 subjects with PTSD, and 58 healthy comparison (HC) subjects, free of current major depression, were studied as inpatients. After a 24-hour urine collection and hourly blood sampling for ambient cortisol determination, a low-dose dexamethasone suppression test was administered, followed by the Trier Social Stress Test. Results The DD group had significantly elevated urinary cortisol compared with the HC group, which was more pronounced in the absence of lifetime major depression, whereas the PTSD and HC groups did not differ. The DD group demonstrated significantly greater resistance to, and faster escape from, dexamethasone suppression compared with the HC group, whereas the PTSD and HC groups did not differ. The three groups did not differ in cortisol stress reactivity, but both psychiatric groups demonstrated a significant inverse correlation between dissociation severity and cortisol reactivity, after controlling for all other symptomatology. The PTSD subgroup with comorbid DD tended to have blunted stress reactivity compared with the HC group. Conclusions The study demonstrates a distinct pattern of HPA-axis dysregulation in DDs, emphasizing the importance of further study of stress-response systems in dissociative psychopathology.