PURPOSE: To evaluate the feasibility of in-vivo 1H magnetic resonance spectroscopy (1H-MRS) for differentiation between hepatic and renal cysts, with emphasis on the analysis of cystic content. MATERIALS AND METHODS: The 1H-MR spectra of 43 cystic lesions (15 hepatic and 28 renal) obtained using in -vivo 1H-MRS at 1.5 T and with a localized proton STEAM sequence were evaluated. We calculated the ratio of the peak area of lipid/water (Rlipid/water), protein/water (Rprotein/water) and lipid/protein (Rlipid/protein), paying particular attention to identifying differences in peak area ratios between the two types of cyst. RESULTS: The 1H-MR spectra from 26.7% (4/15) of hepatic and 67.9% (19/28) of renal cysts showed the lipid peak as most prominent. Mean+/-standard deviations of the Rlipid/water of hepatic and renal cysts were 0.38+/-0.30x10-6 and 8.42+/-23.24x10-6, respectively; for Rprotein/water the corresponding figures were 0.83+/-0.74x10-6 and 1.50+/-2.94x10-6, and for Rlipid/protein, 0.57+/-0.64 and 2.44+/-3.26. All differences were statistically significant (p<0.05), and positive correlation between lipid and protein in hepatic and renal cysts was demonstrated. CONCLUSION: The different in-vivo 1H-MRS findings, for hepatic and renal cysts can be used in comparative study of cystic tumors of the liver and kidney.