Ion chromatography (IC) using chemically suppressed conductivity detection was developed to separate and detect methane- through octanesulfonic acids. Using a gradient borate-acetonitrile mobile phase system on a Dionex PAX-500 column, one is able to resolve the alkylsulfonic acids from most matrix interferents. Resolution was determined for all acid pairs from methane- through octanesulfonic acid. A specific application is described using a SARASEP AN1 column with a borate mobile phase for the assay of methanesulfonic acid (MSA) in a sulfated sugar compound under pharmaceutical investigation. MSA is one constituent used in the synthesis of this sulfated sugar compound. The average method recovery for MSA over the six levels investigated was 102.9% and the average method recovery for sulfate was 92.3%. Method reproducibility was determined over a two-day period with a single sample to be 7.5% and 14% for MSA and sulfate, respectively. The IC method was determined to have a linear response for MSA and sulfate over the working range investigated. The limit of quantification was 0.004% and 0.02% (w/w) for MSA and sulfate, respectively. The limit of detection was 0.0005% and 0.001% for MSA and sulfate, respectively.