Fenn shared the 2002 Nobel Prize in Chemistry with Koichi Tanaka and Kurt Wüthrich "for the development of methods for identification and structure analyses of biological macromolecules." Fenn and Tanaka split half of the award for their work in developing ionization techniques for using mass spectrometry to analyze large biological molecules. Wüthrich was honored for his work in developing nuclear magnetic resonance techniques to analyze similar molecules in solution. Fenn was honoured largely for his contributions to the development of electrospray ionization, which made the analysis of large molecules by mass spectrometry feasible. Fenn's Nobel lecture after being presented with the award was entitled "Electrospray Wings for Molecular Elephants." He was surprised by his selection as a Nobel winner, saying "It's like winning the lottery, I'm still in shock." At the time of his award, Fenn was working at Virginia Commonwealth University. Fenn received his Nobel Prize fairly late in his career. Prior to being honored by the Nobel Foundation, Fenn had received numerous other awards. Early in his career, Fenn's research was focused on molecular beams, leading him to be named an honorary president of the Sixth International Symposium on Molecular Beams in 1977, and the first fellow of the International Molecular Beam Symposium in 1985. In 1982, the Alexander von Humboldt Foundation presented him with their U.S. Senior Scientist Award. Fenn's work in mass spectrometry earned him another spate of awards later in his career. In 1992, the American Society for Mass Spectrometry presented him with their Award for Distinguished Contributions in Mass Spectrometry. The International Society of Mass Spectrometry honored him with the Thomson Medal in 2000, and in the same year the American Chemical Society presented him with the Award for Advancements in Chemical Instrumentation. He was awarded the Association of Biomolecular Resource Facilities Award for outstanding contributions to Biomolecular Technologies in 2002. In 2003, Fenn was honored by his alma mater with the Wilbur Cross Medal, the Yale Graduate School Alumni Association's highest honor. Fenn maintained numerous professional affiliations, including membership in the American Chemical Society, the American Society for Mass Spectrometry, Sigma Chi, the American Association of University Professors and the Alexander von Humboldt Association of America. In 2000, Fenn was made a fellow of the American Academy of Arts and Sciences and in 2003 he was elected to the National Academy of Sciences. Fenn married Margaret Wilson at the end of his second year of graduate studies.