The high abundance of carbohydrates in nature and their diverse roles in biological systems validate the increasing interest for their chemical and biological research. Carbohydrates can be found as monomers or oligomers, or as glycoconjugates, which are formed by an oligosaccharide moiety linked to a protein (glycoproteins) or to a lipid moiety (glycolipids). Blood groups determinants (ABH), tumor associated antigens and pathogen binding sites are some of the relevant glycoconjugates found on mammalian cells. It is well known that carbohydrate and glycoconjugate molecules are implicated in many cellular processes, especially in biological recognition events, including cell adhesion, differentiation and growth, signal transduction, protozoa, bacterial and virus infections as well as immune responses. Therefore, the demand for glycans and glycoconjugates for various studies of targets involved in several serious diseases have been continuously growing. In this chapter we will present the design of drugs based on carbohydrate structure for treatment of parasitic diseases (T. cruzi) and virus infections (influenza and HIV). In addition, the development of glycoconjugate antitumour vaccines related to the structure of human mucin-associated glycans will also be discussed.