A simple, robust, and sensitive liquid chromatography–tandem mass spectrometric (LC–MS/MS) method was developed for the measurement of endogenous adenine in mouse, rat, cynomolgus monkey, and human plasma. A “surrogate analyte” strategy was adopted by employing [13C(U)]-adenine as the surrogate analyte. The plasma samples were processed by protein precipitation, and the extracted supernatant samples were subjected directly to LC–MS/MS analysis. The analysis was carried out in the negative ion detection mode using selected-reaction monitoring (SRM). The method achieved a lower limit of quantification (LLOQ) of 5.0 nM with a signal-to-noise ratio of 10. The intra- and inter-day assay coefficients of variation (CV) were ≤6.67% in rat plasma, and the mean recoveries and matrix effects across species and at various concentrations ranged from 88.8% to 104.2% and 86.0% to 110.8%, respectively. Using this methodology, the endogenous concentration of adenine in plasma of four species was found to range from 8.7 nM in human to 93.1 nM in cynomolgus monkey plasma. The assay was further applied to both an adenine pharmacokinetic study and a pivotal pharmacodynamic study evaluating the plasma concentration of adenine after a dose of 5′-deoxy-5′-methylthioadenosine (MTA).