A sensitive method was developed and validated for simultaneous measurement of an investigational antiviral nucleoside, Amdoxovir (DAPD), its deaminated metabolite 9-(β-D-1,3-dioxolan-4-yl) guanine (DXG), and Zidovudine (ZDV) in human plasma. This method employed high-performance liquid chromatography-tandem mass spectrometry with electrospray ionization. DXG and DAPD separation with sufficient resolution was necessary since they differ in only one mass to charge ratio, which increases the risk of overlapping MS/MS signals. However, the new method was observed to have functional sensitivity and specificity without interference. Samples were purified by ultrafiltration after protein precipitation with methanol. The total run time was 29 min. A linear calibration range from 2 to 3,000 ng mL −1 and 2 to 5,000 ng mL −1 was achieved for DAPD and DXG, and ZDV, respectively. Precisions and accuracies were both ± 15% (± 20% for the lower limit of quantification) and recoveries were higher than 90%. Matrix effects/ion suppressions were also investigated. The analytes were chemically stable under all relevant conditions and the method was successfully applied for the analysis of plasma samples from HIV-infected persons treated with combinations of DAPD and ZDV.