Different degrees of glycosaminoglycan sulfation result in their different charge densities. The charge density differences impact their migration behavior in polyacrylamide gel electrophoresis and size exclusion chromatography, two of the most common methods for determining relative molecular masses of polysaccharides. In this study, we investigated the feasibility of using commercially available heparin oligosaccharides as calibrants for measuring the relative molecular masses of intermediates in a bioengineered heparin process that have different levels of sulfation. A size exclusion chromatography method was established that eliminates this charge density effect and allows the determination of relative molecular mass using a single calibration curve with heparin oligosaccharides calibrants. This is accomplished by overcoming the electrostatic interaction between the glycosaminoglycans and size exclusion chromatography stationary phase using high ionic strength mobile phase.