Rappuoli is the recipient of several prestigious awards, including the Paul Ehrlich and Ludwig Darmstaedter Prize in 1991. He is a member of numerous international associations, including the European Molecular Biology Organization and the American Society for Microbiology. He also serves as a member of the research directors group of the European Commission and was elected to National Academy of Sciences of the United States. He was also awarded the Italian President Gold Medal in 2005 and the Albert Sabin Gold Medal in 2009. In 2013 he was nominated third most influential person worldwide in the field of vaccines by Terrapin. In 2015 he was awarded Fellowship of Imperial College London Faculty of Medicine and the Maurice Hilleman Award.