Vaccination is a highly effective means of disease prevention and has saved countless lives worldwide over the past 200 years. Traditional vaccines based on killed and attenuated organisms and inactivated toxins have constituted the majority of clinically used vaccines to date, but novel vaccines based on subunits of these organisms will be increasingly represented in future. In contrast to attenuated and whole cell vaccines, subunit vaccines do not generally contain immune-stimulatory components and are poorly immunogenic. As a result, new, potent and safe adjuvants and delivery systems are needed to enhance the immunogenicity of these vaccines. Furthermore, there is a drive to replace injected vaccines with those that can be administered by mucosal routes. Since the induction of innate immunity is crucial for vaccines to elicit potent antigen specific immune responses, a greater understanding of innate immunity at mucosal surfaces and the mechanism of action of adjuvants and delivery systems is required.