Practical noninvasive methods for the measurement of absolute metabolite concentrations are key to the assessment of the depletion of myocardial metabolite pools which occurs with several cardiac diseases, including infarction and heart failure. Localized MRS offers unique noninvasive access to many metabolites, but is often confounded by nonuniform sensitivity and partial volume effects in the large, poorly defined voxels commonly used for the detection of low‐concentration metabolites with surface coils. These problems are exacerbated at higher magnetic field strengths by greater radiofrequency (RF) field inhomogeneity and differences in RF penetration with heteronuclear concentration referencing. An example is the ³¹P measurement of cardiac adenosine triphosphate (ATP) and phosphocreatine (PCr) concentrations, which, although central to cardiac energetics, have not been measured at field strengths above 1.5 T. Here, practical acquisition and analysis protocols are presented for the quantification of [PCr] and [ATP] with one‐dimensionally resolved surface coil spectra and concentration referencing at 3 T. The effects of nonuniform sensitivity and partial tissue volumes are addressed at 3 T by the application of MRI‐based three‐dimensional sensitivity weighting and tissue segmentation. The method is validated in phantoms of different sizes and concentrations, and used to measure [PCr] and [ATP] in healthy subjects. In calf muscle (n = 8), [PCr] = 24.7 ± 3.4 and [ATP] = 5.7 ± 1.3 µmol/g wet weight, whereas, in heart (n = 18), [PCr] = 10.4 ± 1.5 and [ATP] = 6.0 ± 1.1 µmol/g wet weight (all mean ± SD), consistent with previous reports at lower fields. The method enables, for the first time, the efficient, semi‐automated quantification of high‐energy phosphate metabolites in humans at 3 T with nonuniform excitation and detection. Copyright © 2013 John Wiley & Sons, Ltd.