Glycosylation is one of the most important posttranslational modification processes, which is regulated by a large number of enzymes. Cell surface, especially mammalian cell surface is heavily coated with glycans. Cell surface glycans are highly related to cell-cell communication, host-pathogen interaction, cell matrix interaction and etc. The aberrations of glycosylation, either intercellular or intracellular, usually indicate the onset of certain diseases, such as cancer and cancer metastasis, thus could be used as biomarkers. Lectin microarray, by far, is the most powerful technologies for high-throughput glycan profiling and comparison. It is highly suitable for both live cell and cell lysate analysis and has the potential for high-throughput, low-cost and fast discovery of glycan related biomarkers. In this review, we will focus on the basic concept and the latest advances of lectin microarray technology. We will emphasize the application of lectin microarrays for biomarker discovery. We will also discuss the challenges that lectin microarrays are facing and the possible future directions. We strongly believe that lectin microarrays will soon become an indispensible and invaluable tool for glycosylation related biomarker discovery.