The mammalian cell surface is rich with carbohydrate polymers involved in a diversity of biological recognition events. Dynamic alterations of surface glycans mediate cell-cell communication in the immune system and host specificity of bacterial and viral pathogens. In addition, altered surface glycosylation has been implicated in disease progression of many cancers and may serve as important new targets for therapeutics. Despite the importance of glycosylation, the systematic analysis of sugars, i.e., glycomics, has lagged behind the well-studied disciplines of genomics and proteomics. This deficiency is due in part to the unique analytical challenges presented by glycans and the overwhelming diversity of sugars in nature. New microarray technologies have provided a high-throughput methods with which to probe the glycome. Our laboratory has pioneered a shown ratiometric two-color lectin microarray method that rapidly evaluates differences in the glycosylation of mammalian cells. Herein, we present a detailed protocol of our lectin microarray methodology for the differential analysis of mammalian glycomes.