A capillary gas chromatographic method using mass spectrometric detection was developed and validated for the trace analysis (ppm level) of methyl methane sulfonate and ethyl methane sulfonate in pharmaceutical drug substances. The method utilizes a capillary column (DB-624) with 6% cyanopropyl phenyl and 94% dimethyl polysiloxane stationary phase. A dissolve-and-injection approach was adopted for sample introduction in a split less mode. Mixture of (80:20) ratio of methanol and chloroform was used as a diluent or sample solvent. A limit of detection of about 0.17 μg/g (0.17 ppm) for methyl methane sulfonate and 0.18 μg/g (0.18 ppm) for ethyl methane sulfonate were achieved and limit of quantitation of 0.52 μg/g (0.52 ppm) for methyl methane sulfonate and 0.54 μg/g (0.54 ppm) for ethyl methane sulfonate were achieved for alkyl sulfonates in drug substance samples.