Baseline and stress-responsive glucocorticoid (GC) levels were assessed during early pregnancy, late pregnancy, and lactation in female variable flying foxes (Pteropus hypomelanus) and in males over the same time period. Animals were maintained in a breeding colony in captivity. High levels of both cortisol and corticosterone were detected, with total plasma GC levels being among the highest documented in vertebrates (up to 3000 ng/ml in individual animals, with cortisol being the primary GC, accounting for approximately 78% of total GCs), and significantly greater in males than in females. Plasma levels of cortisol and corticosterone showed nearly identical profiles within each sex, with the exception of females in late pregnancy, in which corticosterone, but not cortisol, increased significantly. Baseline levels of plasma cortisol were highest in September (when pups were between 1 and 2 months of age) in both sexes, which may be related to the approaching onset of the mating period. There was a continuum in the magnitude of the response to stress (handling and sampling) over time in females, with the greatest stress response in early pregnancy, a dampened response during late pregnancy, and no significant stress response during lactation. Surprisingly, males failed to exhibit elevated GCs after this stress, but did have significant stress-induced hyperglycemia and suppression of plasma testosterone levels. This may be due to their high (perhaps maximal) baseline levels, which suggests that being in a breeding group was chronically stressful for males.