The Athlete Biological Passport (ABP) detects blood doping in athletes through longitudinal monitoring of erythropoietic markers. Mathematical algorithms are used to define individual reference ranges for these markers for each athlete. It is unclear if altitude and exercise can affect the variables included in these calculations in a way that the changes might be mistaken for blood manipulation. The aim of this study was to investigate the influence of the simultaneous strenuous exercise and low to high altitude exposure on the calculation algorithms of the ABP. 14 sea level (SL) and 11 altitude native (ALT) highly trained athletes participated in a 14-day cycling stage race taking place at an average altitude of 2496m above sea level (min. 1014m, max. 4120m), race distances ranged between 96 and 227km per day. ABP blood measures were taken on days -1,3,6,10,14 (SL) and -1,9,15 (ALT) of the race. Four results from three samples of two different SL athletes exceeded the individual limits at the 99% specificity threshold and one value at 99.9%. In ALT, three results from three samples of three different athletes were beyond the individual limits at 99%, one at 99.9%. The variations could be explained by the expected physiological reaction to exercise and altitude. In summary, the abnormalities observed in the haematological ABP's of well-trained athletes during extensive exercise at altitude are limited and in line with expected physiological changes.