An LC-MS/MS method for the trace-level determination of 3-alkyl-2-methoxypyrazines in Sauvignon blanc wines is described. 3-Isobutyl-2-methoxypyrazine (IBMP), 3-isopropyl-2-methoxypyrazine (IPMP) and 3-sec-butyl-2-methoxypyrazine (SBMP) were analyzed by reversed phase liquid chromatography coupled to atmospheric pressure chemical ionization, as electrospray ionization was found to suffer from matrix quenching effects. A sample preparation method involving distillation of wine followed by solvent extraction and sufficient preconcentration was developed. Limits of detection and quantification for all three analytes were 0.03 ng/L and 0.10 ng/L, respectively, making the method more sensitive than gas chromatographic methods. IBMP was found to be the most abundant congener in South African Sauvignon blanc wines, with concentrations varying between 0.40 and 44 ng/L in 575 samples. IPMP and SBMP levels varied from <0.03 to 3.9 and <0.03 to 3.2 ng/L, respectively. Statistical investigation indicated no clear correlation between methoxypyrazine content and either geographical origin or vintage. The method was also successfully applied for the quantitation of IBMP in five additional South African wine varieties, including three red wine cultivars. The developed method represents a powerful new tool for the in-depth investigation of these important wine aroma constituents.