The level of tissue oxygenation provides information related to the balance between oxygen delivery, oxygen utilization, tissue reactivity and morphology during physiological conditions. Tissue partial pressure of oxygen (PtO 2 ) is influenced by the use of anesthesia or restraint. These factors may impact the absolute level of PtO 2 . In this study we present a novel fibre optic method to measure brain PtO 2 . This method can be used in unanesthetized, unrestrained animals, provides absolute values for PO 2 , has a stable calibration, does not consume oxygen and is MRI compatible. Brain PtO 2 was studied during acute hypoxia, as well as before and after 28 days of high altitude acclimatization. A sensor was chronically implanted in the frontal cortex of 8 Wistar rats. It is comprised of a fiber optic probe with a tip containing material that fluoresces with an oxygen dependent lifetime. Brain PtO 2 declines by 80% and 76% pre-and post-acclimatization respectively, when the fraction of inspired oxygen declines from 0.21 to 0.08. In addition, a linear relationship between brain PtO 2 and inspired O 2 levels was demonstrated r 2 =0.98 and r 2 =0.99 (pre-and post-acclimatization). Hypoxia acclimatization resulted in an increase in the overall brain PtO 2 by approximately 35%. This paper demonstrates the use of a novel chronically implanted fibre optic based sensor for measuring absolute PtO 2 . It shows a very strong linear relationship in awake animals between inspired O 2 and tissue O 2 , and shows that there is a proportional increase in PtO 2 over a range of inspired values after exposure to chronic hypoxia.