We report a significantly more rapid method for quantitation of the urinary mercapturic acids of the isomeric toxicants crotonaldehyde, methacrolein, and methyl vinyl ketone. The major innovation of this novel method is detection by liquid chromatography-negative atmospheric pressure chemical ionization-tandem mass spectrometry-selected reaction monitoring as opposed to detection by negative electrospray ionization in our previously reported method. The new method also uses an improved Raptor Biphenyl HPLC column. The total chromatographic analysis time was reduced to about 8 min compared to 35 min in our previously published method. Accuracy, precision, and ruggedness of the new method were established, and its suitability for the analysis of urine samples from 2500 cigarette smokers and non-smokers was confirmed. The improved method is practical for quantitation of these important toxicants in clinical studies requiring analysis of thousands of urine samples.