In this [15O]-water PET/MRI study, we compared two non-invasive MRI techniques to measure brain oxygen extraction fraction (OEF) in 10 patients with Moyamoya disease, a steno-occlusive disease of arteries at the base of the brain. Relative OEF from magnetic susceptibility in veins and tissue R2' inversely correlated with [15O]-water PET baseline cerebral blood flow and cerebrovascular reactivity (after vasodilation with acetazolamide). Susceptibility-based OEF in veins was abnormally elevated by 20.4% in regions with severe stenosis compared to healthy tissue. R2' maps showed a smaller OEF elevation (9.6%) that may be confounded by other physiological changes (e.g. blood volume) in disease.