Tauxe's research interests include bacterial enteric diseases, epidemiology and pathogenesis of infectious diseases, epidemiological and clinical consequences of bacterial genetic exchange, antimicrobial use and resistance to antimicrobial agents, and teaching epidemiological methods. He has participated in or supervised numerous domestic and overseas epidemiological investigations all over the world, most notably the 1984 Rajneeshee bioterror attack, the 2008 United States salmonellosis outbreak, the 2010-2013 Haiti cholera outbreak, establishment of Pulsenet, and the West African Ebola virus epidemic.