AbstractThe effect of hypoxia (inspired oxygen fraction, F1O2of 10% and 16%) and hyperoxia (F1O2) of 100%) on gradient echo images of the brain using long echo times was investigated in six healthy volunteers (age 24‐28 years). Different flip angles were used with an F1O2of 10% to assess the importance of saturation effects. The total cerebral blood flow was measured by a phase mapping technique during normoxia as well as hypoxia (F1O2of 10% and 16%) and hyperoxia (F1O2of 50% and 100%). High relative signal changes were found, independently of the flip angle, with F1O2of 10%. With a flip angle of 40° the values of δR2* for cortical grey matter, central grey matter, white matter and the sagittal sinus were 0.79, 0.41, 0.26 and 3.00/s; with a flip angle of 10° the corresponding values were 0.70, 0.37, 0.24 and 3.15/s. The total cerebral blood flow increased by 41% during inhalation of 10% O2and decreased by 27% during 100% O2; no flow changes were seen during moderate changes in F1O2. It is concluded that flow effects play a minor role for fMRI signal strength in this application since (i) they did not abolish the signal changes caused by changes in blood oxygenation during hyper‐ and hypoxia, (ii) the observed signal changes were closely related to the changes in arterial oxygen saturation during hypoxia and (iii) the signal changes were little affected by changing the flip angle from 40