The first year practising medicine, pre-registration, is considered to be a stressful time for junior doctors. The aims of this study were to explore how levels of psychological distress were affected by changes in the working environment and to examine these effects across subjective (i.e. self-report) and objective (i.e. stress hormone cortisol) indices of psychological distress. A cohort of 36 pre-registration house officers (males = 15) completed a battery of psychosocial measures and collected salivary samples for the measurement of diurnal cortisol at the beginning and end of a 3-4-month clinical rotation with the assumption that the end of a rotation would be less stressful than the beginning. Results from the self-report measures remained constant over the two-time points suggesting no perceived change in emotional well-being on a subjective level. However, there is some evidence of neuro-endocrine changes across the two time points suggestive of hypothalamic-pituitary-adrenal axis dysregulation. In particular, there was a significant difference between the cortisol awakening rise with the greatest rise seen at the beginning of a rotation. In addition, the daily cortisol decline (diurnal slope) was also significantly less at this test time. These findings have implications for the discord apparent between self-report and physiological measures of psychological stress.