• 2001: Spinoza Prize. 
• 2004: Louis-Jeantet Prize for Medicine. 
• 2005: the Science and Society Prize. 
• 2006: Rabbi Shai Shacknai Memorial Prize for Immunology and Cancer Research. 
• 2008: Josephine Nefkens Prize for Cancer Research (Erasmus MC, Rotterdam). 
• Editorial board member of (a.o): EMBO Journal, EMBO reports, Cell, Gastroenterology.
• 2009: Dutch Cancer Society Award (Queen Wilhelmina Research Prize)
• 2012: Dr. A.H. Heineken Prize for Medicine
• 2012: Appointed Knight of the Order of the Netherlands Lion
• 2014: Massachusetts General Hospital Award in Cancer Research
• 2014: Fellow of the AACR Academy
• 2014: Struyvenberg European Society for Clinical Investigation (ESCI) medal
• 2014: National Icon of the Netherlands
• 2015: ISSCR-McEwen Award for Innovation in 2015
• 2016: Member of the Academie des Sciences de I 'Institut de France
• 2016: Kazemi Award for Research Excellence in Bio-Medicine
• 2016: The Körber European Science Prize, Germany
• 2016: Swammerdam medaille, Amsterdam
• 2016: The Ilse & Helmut Wachter award, Hamburg, Germany
• 2016: Royal Netherlands Academy of Arts and Sciences Professor Prize
• 2017: President of the International Society for Stem Cell Research (ISSCR)
• 2017: Princess Takamatsu Award of Merit, Tokyo
• 2017: Großes Verdienstkreuz mit Stern, Germany 
• 2018: Academia Europaea Erasmus Medal, Barcelona, Spain
• 2019: Keio Medical Science Prize, Tokyo, Japan

Een (vrijwel) volledige lijst van onderscheidingen en prijzen toegekend aan prof. dr. Hans Clevers is te vinden op de aan hem gewijde pagina op Wikipedia.