The mammalian immune system has evolved to protect the body from invading parasites, bacteria and viruses. As increased knowledge about host–pathogen interactions undoubtedly holds clues for improving the treatment of infection, the investigation of how the immune system interfaces with pathogens is of paramount interest to immunologists. In this issue, the underlying mechanisms of antiviral immunity are explored from several angles: on page 594, Yong-Jun Liu and colleagues discuss the key role of plasmacytoid dendritic cells in immunity against viruses and on page 619, Philip Goulder and David Watkins review the influence of host MHC molecules on HIV infection. Recent advances in the sophistication of molecular techniques have permitted immunologists to examine the blueprints that underlie host–pathogen interactions more closely than ever before. On page 644, Michael Katze and colleagues describe new insights into the pathogenesis of RNA viruses that have been made possible by the use of functional genomics.

The power of genomic approaches is also rapidly advancing our understanding of other aspects of immunology. On page 631, Ramnik Xavier and John Rioux discuss how genome-wide association studies have allowed researchers to make leaps and bounds in the discovery of factors that contribute to autoimmune diseases, helping to shed new light on questions that have puzzled immunologists for decades.

Central to all types of immune response is the processing and presentation of antigens by innate immune cells. On page 607, Hidde Ploegh and colleagues provide an overview of the numerous complex pathways of subcellular antigen trafficking. A broader understanding of these concepts provides a platform on which increased knowledge about pathogen defence, autoimmune processes and other types of immune response can be explored.