OBJECTIVE: To determine whether the level of metabolites in magnetic resonance spectroscopy (MRS) is a representative marker of underlying pathological changes identified in positron emission tomographic (PET) images in Alzheimer disease (AD). METHODS: We performed PET-guided MRS in cases of probable AD, mild cognitive impairment (MCI), and healthy controls (HC). All participants were imaged by 11 C-Pittsburgh compound B (11 C-PiB) and 18 F-fluorodeoxyglucose (18 F-FDG) PET followed by 3T MRS. PET images were assessed both visually and using standardized uptake value ratios (SUVRs). MRS voxels were placed in regions with maximum abnormality on amyloid (Aβ+) and FDG (hypometabolic) areas on PET scans. Corresponding normal areas were selected in controls. The ratios of total N-acetyl (tNA) group, myoinositol (mI), choline, and glutamate + glutamine over creatine (Cr) were compared between these regions. RESULTS: Aβ + regions had significantly higher (p = 0.02) mI/Cr and lower tNA/Cr (p = 0.02), whereas in hypometabolic areas only tNA/Cr was reduced (p = 0.003). Multiple regression analysis adjusting for sex, age, and education showed mI/Cr was only associated with 11 C-PiB SUVR (p < 0.0001). tNA/Cr, however, was associated with both PiB (p = 0.0003) and 18 F-FDG SUVR (p = 0.006). The level of mI/Cr was not significantly different between MCI and AD (p = 0.28), but tNA/Cr showed significant decline from HC to MCI to AD (p = 0.001, p = 0.04). INTERPRETATION: mI/Cr has significant temporal and spatial associations with Aβ and could potentially be considered as a disease state biomarker. tNA is an indicator of early neurodegenerative changes and might have a role as disease stage biomarker and also as a valuable surrogate marker for treatment response. Ann Neurol 2018;83:771-778.