Glycosylation is chemically the most complex post-translational modification of proteins and therefore understanding the structural and biological implications of post-translational glycosylation is a major challenge. The need for rapid and reliable investigations of protein-glycan interaction events and the substantial efforts required to synthesize glycans and glycopeptides with a variety of structures has called for the development of miniaturized analytical techniques. In the last decade, glycan and glycopeptide microarrays have enabled high-throughput analysis of diverse protein-glycan interactions. Evaluations of enzyme activities and substrate specificities, characterization of glycan binding proteins, mapping of antibody epitopes, detection of autoantibodies and serodiagnosis are typically conducted on microarrays. The most significant developments in synthesis, immobilization and applications of glycopeptide microarrays are covered in this review.