A simple, sensitive and robust method using HILIC–ESI-MS has been developed for the determination of methane sulfonic acid (MSA) at low ppm level in order to verify the effectiveness of controlling the formation of genotoxic sulfonate esters in the downstream synthetic step, by which produces active pharmaceutical ingredient (API). Stationary phases with positively charged functional groups such as triazole and amino phases were evaluated for the retention of alkyl sulfonic acids. The MSA was quantitated at 1–10 ppm relative to the API using a Cosmosil column (triazole stationary phase) in HILIC mode and the control of MSA can be monitored effectively using the HILIC–ESI-MS methodology. In addition, to provide general guidance for the HILIC–ESI-MS method development, the retention behavior of propanesulfonic acid (PSA) in HILIC mode was investigated using a Unison UK-Amino column to have a better understanding of the HILIC separation mechanism. The results showed reasonable evidence that the combined effect of surface adsorption and ion-exchange played a dominant role for sulfonic acids when using a mobile phase within typical HILIC operation range (0.05–0.20 aqueous volume fraction) while the ion-exchange effect becomes increasingly important in a mobile phase with higher water content. The advantage of using ESI-MS detection in HILIC mode was also demonstrated by the observation that the sensitivity of PSA increased substantially with increasing acetonitrile fraction in mobile phase from 0.80 to 0.95.