*1988 Japan IBM Science Prize
*1992 Chu-Nichi Culture Award
*2002 Medals with Purple ribbon
*2003 Fellow of the American Association for the Advancement of Science (AAAS)
*2004 Yamada-Koga Prize
*2006 Tetrahedron Prize for Creativity in Organic Chemistry & BioMedicinal Chemistry
*2007 Japan Academy Prize (academics)
*2007 Humboldt Prize
*2011 The Ryoji Noyori Prize
*2012 Fujihara Award
*2017 The Roger Adams Award (American Chemical Society)
*2018 Person of Cultural Merit