A sensitive and selective method is presented to accurately determine the level of protein-bound 3-nitro-l-tyrosine (NTyr) in rat plasma and kidney samples. This assay is based on isotope dilution liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). The sample preparation entails protein precipitation, acid hydrolysis with 6 N HCl, and solid-phase extraction (using reverse and aminopropyl phase cartridges) prior to the determinative step. For kidney samples, NTyr is converted into its butyl ester to improve sensitivity. The potential formation of artifactual NTyr during the acid hydrolysis step was carefully followed and determined by supplementation of the samples with ¹³C-labeled l-tyrosine (Tyr) prior to protein digestion. Hence, the concomitant measurement of formation of ¹³C-enriched NTyr enabled the accurate determination of artifactual NTyr. This approach was employed to measure the basal level of protein-bound NTyr in rat plasma and kidney samples, revealing levels in the range of 4−18 μmol/mol of Tyr and 50−68 μmol/mol of Tyr, respectively. No artifactual nitration of Tyr was observed in kidney proteins, whereas in the case of plasma the contribution of the artifactual response ranged from 16 to 40%. This method allows the analysis of protein-bound NTyr with a full control of the artifactual nitration of tyrosine during the proteolysis and/or sample preparation. Reliable detection of NTyr in proteins may allow insight into the role of nitric oxide-derived oxidants under various pathological conditions.