Major Depressive Disorder (MDD) is one of the leading causes of global disability, yet the underlying biological mechanisms for this disorder are not well understood. The amygdala, as the key emotion maker in the brain, is known to have a role in MDD. Amygdalar dysfunction has been hypothesised to drive the aberrant hypothalamic-pituitary-adrenal (HPA) stress responses that are known in the disorder. The stria terminalis (ST) as the principal white matter tract connecting the amygdala to the hypothalamus may also have a role in MDD. 15 patients with MDD and 20 matched healthy controls underwent advanced diffusion-weighted magnetic resonance imaging at Trinity College Institute of Neuroscience. Using constrained spherical deconvolution tractography and a novel anatomically-driven protocol, the ST was isolated. Morning salivary cortisol samples (0, 30 and 60 minutes after waking) were obtained from all participants and cortisol concentrations determined using liquid chromatography-mass spectroscopy. The cortisol awakening response (CAR) was calculated using formulae for the area under the curve. Analysis of covariance (ANCOVA) between depressed and controls revealed no difference for whole ST metrics. Multivariate ANCOVA along discrete sections of the tract showed increased mean and radial diffusivity (p-values of 0.019 + 0.036 and 0.022 + 0.041 respectively) in the portion of the ST close to the amygdala in MDD patients. Split-group partial correlations revealed an inverse relationship of the length (p-value of 0.003) and volume (p-value of 0.032) of the left ST with the CAR. Similarly, mean diffusivity, radial diffusivity and fractional anisotropy showed associations with the CAR along key sections of the tract. These novel findings suggest that changes in the ST may account for neuroendocrine disturbances in MDD. Alterations in diffusion metrics may reflect diverse pathology including axonal degeneration and demyelination along sections of the tract. These findings suggest that the connection between the amygdala and hypothalamus may be functionally altered resulting in abnormal cortisol secretion and stress responses in MDD.