Carbohydrates and glycoconjugates are involved in a number of biological processes including host-pathogen interactions, cell communication, proliferation and differentiation as well as the initiation of immune responses. However, access to synthetic oligosaccharide structures has been limited for long time since no standardized protocols for the synthesis of complex oligosaccharides from monomeric building block existed. Recent advances in glycochemistry and glycobiology have helped elucidate biological functions of carbohydrates. Novel methods such as automated synthesis of vaccine candidates and immunologically relevant carbohydrates have contributed to this success as well as high-throughput methods such as glycan arrays. This review illustrates the impact of carbohydrate synthesis on the design of efficient carbohydrate-based antimicrobial and anticancer vaccines. Furthermore, this review focuses on how immunological research can benefit from these novel tools provided by glycochemistry.