Cell surfaces, especially mammalian cell surfaces, are heavily coated with complex poly- and oligosaccharides, and these glycans have been implicated in many functions, such as cell-to-cell communication, host-pathogen interactions and cell matrix interactions. Not surprisingly then, the aberrations of glycosylation are usually indicative of the onset of specific diseases, such as cancer. Therefore, glycans are expected to serve as important biomarkers for disease diagnosis and/or prognosis. Recent development of the lectin microarray technology has allowed researchers to profile the glycans in complex biological samples in a high throughput fashion. This relatively new tool is highly suitable for both live cell and cell lysate analyses and has the potential for rapid discovery of glycan-based biomarkers. In this review, we will focus on the basic concepts and the latest advances of lectin microarray technology. We will also emphasize the application of lectin microarrays for biomarker discovery, and then discuss the challenges faced by this technology and potential future directions. Based on the tremendous progress already achieved, it seems apparent that lectin microarrays will soon become an indispensible tool for glycosylation biomarker discovery.