This review summarizes progress in analysis of glycosaminoglycans using mass spectrometry (MS) approaches. The specific areas covered include analytical challenges, disaccharide analysis, top-down and bottom-up techniques, sequence analysis, and future perspectives. A brief outline of the complexity and heterogeneity of these unique saccharides and their analysis is provided along with examples of several recent studies. Unique problems and challenges in the characterization of glycosaminoglycans are discussed along with many of the analytical tools used in particular MS methods and the types of information provided. Advances in MS-related technologies have provided more sensitive and accurate detection and sequence analysis of this complex and chemically unique class of bioconjugates. Effective MS-based methods and automated data handling with bioinformatics tools have been developed for disaccharide analysis, top-down and bottom-up analysis, and sequencing studies of relatively short oligosaccharides. It is envisioned that further improvements in MS technologies along with bioinformatics methods will make sequencing studies of longer glycosaminoglycan chains easier and faster.