There is growing interest in the potential interactions between infant vaccination and risk for development of atopic disease. The aspect of this issue which has dominated this debate concerns suggestions that infant vaccination may stimulate allergic sensitisation. These suggestions derive from retrospective epidemiological analyses and will remain speculative unless they can be confirmed in prospective studies, particularly as conflicting findings have been reported. However, there is a potentially more important issue surfacing in this debate, which entails the converse situation, i.e. that genetic risk for atopy influences capacity to respond to vaccination during infancy. Support for the latter possibility comes from recent studies on the role of developmental factors which determine immune competence during infancy, and attendant risk for inflammatory and infectious diseases. The relevant findings are reviewed briefly below.