The physical, mental and emotional stresses experienced during the training and careers of physicians have been linked to increased rates of anxiety, depression and suicide. Increased stress leads to alterations in the hypothalamic–pituitary–adrenal (HPA) axis, which can determine multisystem modulations with acute and chronic consequences. This study investigated salivary cortisol patterns in third-year medical students performing clinical work at a US medical school. Morning and evening salivary cortisol samples were collected from students during the last 2 weeks of each of three successive clinical rotations and while on vacation. Salivary cortisol levels were measured using Siemens radioimmunoassay kits (Siemens Medical Solutions Diagnostics, Los Angeles, CA, USA). Statistical analysis used mixed-effects regression models. Eleven students submitted 64 salivary samples. Statistically significant blunting of the diurnal cortisol variation was observed in students on inpatient rotations. HPA axis changes occur in third-year medical students performing inpatient clinical work. These findings can inform curriculum planning, rotation-specific guidelines and the development of student wellness programmes. Copyright © 2011 John Wiley & Sons, Ltd.