Functional immunomics promises great rewards, both in terms of our basic understanding of the immune system and in disease diagnosis/prognosis and rational epitope-driven vaccine design. Research into the basic biology and statistical methods associated with functional immunomic experiments will lead to the advancement of medical science and public health. Functional immunomics is however still at an early stage of development. In this review we have attempted to provide a coherent vision of this nascent field, and have speculated on future research directions for this technology.