Adults with fibromyalgia syndrome report high rates of childhood trauma. Neuroendocrine abnormalities have also been noted in this population. Exploratory analyses tested relationships between retrospective reports of childhood trauma and diurnal salivary cortisol patterns among 85 women with fibromyalgia. Subjects with fibromyalgia completed self-reports of childhood physical, sexual and emotional abuse, as well as emotional and physical neglect. Recent major life events, current perceptions of stress, and depressive symptoms were also assessed. Salivary cortisol was collected six times per day for two consecutive days to assess diurnal rhythm, awakening response and mean cortisol levels. Hierarchical regression analyses were performed, controlling for age, relevant medications, life events, perceived stress, and depressive symptoms. Childhood physical abuse predicted flattened diurnal cortisol rhythms as well as greater cortisol responses to awakening. Sexual abuse was a second predictor of increased awakening cortisol responses. Patients with a history of trauma had markedly low levels of cortisol at the time of first awakening, partly explaining the results. These findings suggest that severe traumatic experiences in childhood may be a factor of adult neuroendocrine dysregulation among fibromyalgia sufferers. Trauma history should be evaluated and psychosocial intervention may be indicated as a component of treatment for fibromyalgia.