Historical accounts reveal that influenza viruses, which cause a highly contagious acute respiratory illness in humans, have likely been with us for centuries. Epidemics of varying severity occur almost annually in temperate climates and are punctuated by the much less frequent but more dramatic occurrence of pandemic influenza. Studies of the molecular epidemiology of influenza viruses have yielded insights that are critical to our current understanding of how novel human influenza viruses emerge from the gene pool present among lower animals to cause pandemics of influenza. These studies have also contributed to our understanding of how these viruses, once present in the human population, are able to escape host immune surveillance and thus cause successive infections with related influenza viruses in the same individual.