Heparan sulfate (HS) is a complex oligosaccharide that is a marker of a number of diseases, most notably several of the mucopolysaccharidoses (MPS). It is a very heterogeneous compound and its quantification at physiological concentrations in patient samples is challenging. Here, we demonstrate novel derivatization chemistry for depolymerization/desulfation and alkylation of HS based on butanolysis. The resultant alkylated disaccharides are quantifiable by LC-MS/MS. This new method is at least 70-fold more sensitive than a previously published methanolysis method. Disaccharide yield over time is compared for methanolysis, ethanolysis, and butanolysis. Maximum disaccharide concentration was observed after 2 h with butanolysis and 18 h with ethanolysis whereas a maximum was not reached over the 24 h of the experiment with methanolysis. The sensitivity of the new technique is illustrated by the quantification of HS in 5 μL urine samples from MPS patients and healthy controls. HS was quantifiable in all samples including controls. Disaccharide reaction products were further characterized using exact mass MS/MS.