The amygdala plays a central role in emotional processing and has an activating influence on the hypothalamic-pituitary-adrenal (HPA) axis. Structural changes in the amygdala have been associated with early adversity and, in principle, may contribute to the later emergence of emotional pathologies by influencing the way that the brain responds to stress provocation. The present study examined the relationship between amygdala volumes and cortisol secretion in response to a social stressor among young adults who were or were not exposed to maternal postnatal depression (PND) early in development (referred to as PND offspring and controls, respectively). Hierarchical Linear Modelling (HLM) revealed that, on a sample-wide level, there was no evidence of a relationship between total amygdala volume, or the volume of the right or left hemisphere amygdala taken separately, and cortisol reactivity. Unexpectedly, for PND offspring, larger right hemisphere amygdala volume was associated with lower cortisol reactivity in response to stress, an effect that was not apparent in control offspring. We conclude that the relationship between amygdala volumes and stress reactivity may not be as clear as previous models suggested.