Abstract Background Although atrial function has prognostic significance in many cardiovascular conditions, changes during exercise have not previously been assessed. The aim of this study was to evaluate left atrial (LA) and right atrial (RA) volume and function during incremental exercise, both in normal individuals, healthy athletes, and in patients with chronic thromboembolic pulmonary hypertension (CTEPH). Methods Fifteen healthy non-athletes, 15 athletes and 15 CTEPH patients underwent multi-slice real-time cardiovascular magnetic resonance imaging at rest and during supine bicycle exercise with simultaneous invasive hemodynamic measurements. Results At rest, athletes had larger indexed maximal RA and LA volumes (iRAVmax, iLAVmax) than CTEPH patients and non-athletes, the latter two groups having similar values. CTEPH patients had lower RA and LA emptying functions (EmF) at rest. During exercise, RA volumes (maximum and minimum) increased in CTEPH patients, whilst decreasing in athletes and non-athletes (P