Over the last 10 years, glycan microarray technology has emerged as a powerful high-throughput tool for studying the interactions of carbohydrates with a variety of biomolecules. The array format allows one to screen thousands of binding interactions in a single experiment using minimal amounts of scarce materials. More recently, this technology has been applied to the discovery of biomarkers for diagnosis, prognosis, risk prediction, and monitoring immune responses. Biomarker discovery using glycan arrays has primarily focused on monitoring changes to the anti-glycan antibody repertoires in serum, since the populations of antibodies can change significantly with the onset of disease, exposure to pathogens, or vaccination. Herein, we review efforts to use glycan arrays to identify new biomarkers for cancer, infections, autoimmune diseases, and immune responses.