Influenza viruses continually circulate and cause yearly epidemics, which kill 20,000 people in an average year in the United States. Occasionally and unpredictably, pandemic influenza strains sweep the world, infecting 20% to 40% of the world's population in a single year. In 1918, the worst influenza pandemic on record caused 675,000 deaths in the United States and up to 40 million deaths worldwide. Despite the prevalence of this virus, molecular assays for influenza diagnosis, surveillance, vaccine strain selection, and research have lagged behind such assays for other common viral pathogens. The extreme genetic variability of influenza viruses makes the design of useful molecular-based assays challenging, but several different approaches have been successfully used. RT-PCR is effective for the initial diagnosis and has greater sensitivity than other available rapid assays. Molecular assays also can be used to subtype influenza isolates, and sequence analysis of hemagglutinin may assist greatly in surveillance studies and vaccine strain selection. RT-PCR for influenza also can be performed from tissue biopsy specimens for both retrospective diagnosis and research.