Background: Aircraft cabins are pressurized to maximum effective altitudes of 2440m, resulting in significant decline in oxygen saturation in crew and passengers. This effect has not been studied in athletes. Objective: To investigate the degree of decline in oxygen saturation in athletes during long-haul flights. Methods: A prospective cross sectional study. National level athletes were recruited. Oxygen saturation and heart rate were measured with a pulse oximeter at sea level before departure, at 3 and 7 hours into the flight and again after arrival at sea level. Aircraft cabin pressure and altitude, cabin fraction of inspired oxygen and true altitude were also recorded. Results: 45 athletes and 18 healthy staff aged between 17 and 70 years were studied on 10 long-haul flights. Oxygen saturation levels declined significantly after 3 hours and 7 hours (3-4%), compared to sea level values. There was an associated drop in cabin pressure and fraction of inspired oxygen and increase in cabin altitude. Conclusions: Oxygen saturation declines significantly in athletes during long-haul commercial flights, in response to reduced cabin pressure. This may be relevant for altitude acclimatization planning by athletes, since the time spent on the plane should be considered time already spent at altitude, with associated physiological changes. For flights of 10 to 13 hours duration, it will be difficult to arrive on the day of competition to avoid the influence of these changes, as is often suggested by coaches.