The carbohydrate moieties displayed by pathogenic protozoan parasites exhibit many unusual structural features and their expression is often developmentally regulated. These unique structures suggest a specific relationship between such carbohydrates and parasite pathogenicity. Studies of infected humans indicate that immune responses to protozoan parasites are elicited by glycan determinants on cell-surface or secreted molecules. Infections by protozoa are a major worldwide health problem, and no vaccines or efficacious treatments exist to date. Recent progress has been made in elucidating the structure and function of carbohydrates displayed by major protozoan parasites that infect man. These structures can be used as prototypes for the chemical or combined chemo-enzymatic synthesis of new compounds for diagnosis and vaccine development, or as inhibitors specifically designed to target parasite glycan biosynthesis.