RATIONALE AND OBJECTIVES: To evaluate whether decoupling improves signal-to-noise ratio and frequency resolution of in vivo kidney spectra, and to compare native and well-functioning transplant kidneys. METHODS: Proton decoupling in conjunction with three-dimensional chemical shift imaging (3D-CSI) in phosphorus-31 magnetic resonance (MR) spectroscopy was used with a spatial resolution of 64 cm3 and 17-minute acquisition time to compare native (n = 10) and well-functioning transplant (n = 9) kidneys. RESULTS: Proton decoupling improved peak amplitudes by almost 30%, as well as chemical shift resolution of in vivo kidney spectra. No statistically significant differences in phosphometabolite ratios and renal spectra were observed between healthy volunteers and patients with nonrejecting transplants. The phosphodiester-phosphomonoester ratio was 3.02 +/- 0.88, phosphomonoester-inorganic phosphate ratio was 1.07 +/- 0.44, and inorganic phosphate-adenosine triphosphate ratio was 0.58 +/- 0.22 after correction for saturation effects. CONCLUSION: Improved spectra of native and transplant kidneys can be obtained in vivo with MR spectroscopy by using a short acquisition time.