Glycosylation is a critical quality attribute of biotherapeutics produced from mammalian cells. Small changes in the glycan structures may have profound effects on the efficacy and functions of the glycoprotein, such as fucosylation of the IgG glycan reducing the ability of the IgG to bind to the FcϒRIIIA receptor. Chinese hamster ovary produced glycoprotein biotherapeutics may contain antigenic glycan structures that must be defined and monitored. Therefore, structural analysis of glycans is a key component in the development and production of glycosylated products. We discuss the current techniques available for glycan, glycopeptide and whole glycoprotein analysis. We emphasize recent analytic developments in high-throughput automated methods, as well as, further refinement of methods for separation and identification of isomers and potentially antigenic structures.