- 2018/05 - Japan IDDM network 1st Yamada Kazuhiko Prize
- 2018/03 - Japan Broadcasting Corporation The 69th NHK Broadcasting Culture Award
- 2015/11 - Academy of Sciences, Institute de France Elected as a Foreign Associate of Academy of Sciences
- 2015/10 - The National Academy of Medicine Elected as an International Member of the National Academy
- 2015/09 - University of California, San Francisco UCSF 150th Anniversary Alumni Excellence Awards
- 2015/02 - Glaucoma Research Foundation The Visionary Award by Glaucoma Research Foundation
- 2014/07 - Japan Association of New Economy JANE Innovation Award 2014
- 2014/06 - The Rockefeller University Honorary degree by the Rockefeller University
- 2013/12 - The Japan Academy Elected to the Japan Academy as a member
- 2013/11 - Japan Society of Northern California World Visionary Award
- 2013/09 - Kyoto Prefecture Special Honor Award of thr Kyoto Medical Association
- 2013/06 - Kyoto University the 2013 Kyoto University Shi-Shi Award
- 2013/04 - Amyotrophic lateral sclerosis (ALS) Association Golden West Chapter “Commitment to a Cure” Award
- 2013/02 - Milner Foundation 2013 Breakthrough Prize in Life Sciences
- 2012/12 - Novel Foundation The Nobel Prize in Physiology or Medicine 2012
- 2012/11 - Japanese Government Order of Cultural Merit, Japan
- 2012/04 - Technology Academy Finland The Millennium Technology Grand Prize, Technology Academy Finland
- 2011/10 - Massachusetts General Hospital The 2011 Warren Triennial Prize of Massachusetts General Hospital (MGH)
- 2011/06 - International Society for Stem Cell Research 2011 ISSCR McEwen Centre Award for Innovation
- 2011/06 - Japan Society of Boston 2011 Distinguished Leadership Award, Japan Society of Boston
- 2011/06 - BBVA Foundation 2010 BBVA Foundation Frontiers of Knowledge Award in the Biomedicine category, Spain
- 2011/05 - Wolf Foundation 2011 Wolf Prize in Medicine
- 2011/05 - National Academy of Sciences Elected to National Academy of Sciences as Foreign Associate
- 2011/05 - Albany Medical Center 11th Annual Albany Medical Center Prize in Medicine and Biomedical Research
- 2011/03 - King Faisal Foundation King Faisal International Prize for Science (Medicine) 2011
- 2010/11 - International Balzan Foundation 2010 Balzan Prize for Stem Cells: Biology and Potential Applications
- 2010/11 - Inamori Foundation 26th annual Kyoto Prize in Advanced Technology, Japan
- 2010/11 - Japanese Government 2010 Person of Cultural Merit, Japan
- 2010/11 - Japan Medical Association Medical Award of the Japan Medical Association, Japan
- 2010/06 - The Japan Academy 100th Imperial Prize and Japan Academy Prize, The Japan Academy, Japan
- 2010/05 - The Japanese Orthopaedic Association 社団法人 日本整形外科学会 特別学術会員賞
- 2010/05 - March of Dimes Foundation 2010 March of Dimes Prize in Developmental Biology
- 2009/10 - Gairdner Foundation 2009 Canada Gairdner International Award
- 2009/10 - The Lasker Foundation 2009 Albert Lasker Basic Medical Research Award
- 2009/04 - Nikkei Business Publications, Inc. Nikkei BP Technology Award, Nikkei Business Publications, Inc., Japan
- 2009/03 - Brandeis University Lewis S. Rosenstiel Award
- 2009/03 - The Japanese Pharmacological Society 第2回日本薬理学会 江橋節郎賞
- 2009/03 - The Uehara Memorial Foundation Uehara Award
- 2009/02 - The Shimadzu Science Foundation 2008 Shimadzu Award
- 2008/11 - Foundation for Promotion of Material Science and Technology of Japan 8th The Yamazaki Teiichi Prize
- 2008/11 - The Kyoto Shimbun Co., Ltd. Kyoto Newspaper Taisho, Japan
- 2008/11 - University of Southern California Meira and Shaul G. Massry Prize
- 2008/11 - The Robert Koch Foundation Robert Koch Prize 2008
- 2008/11 - Japanese Government Medals of Honor from the Japanese Government (“Shiju Hosho”, Medals with Purple Ribbon), Japan
- 2008/11 - Takeda Science Foundation Takeda Prize for Medical Science, Japan
- 2008/10 - American Skin Association American Skin Association 10th Annual Gala, 2008 Lifetime Scientific Achievement Award
- 2008/09 - Kyoto Prefecture/Kyoto City Kyoto Souzousya Taisho Awards, Special Prize, Japan
- 2008/09 - Shaw Prize Foundation Shaw Prize in Life Science and Medicine 2008
- 2008/07 - The Sixth Takamine Memorial Sankyo Prize, Japan
- 2008/05 - Chunichi Newspaper Co. Chunichi Cultural Prize, Chunichi Newspaper Co., Japan
- 2008/04 - MEXT, Japan The Special Prize for Science and Technology, the Minister of Education, Culture, Sports, Science and Technology, Japan
- 2008/04 - Nikkei Business Publications, Inc. Nikkei BP Golden Award, Nikkei Business Publications, Inc., Japan
- 2008/02 - Inoue Foundation for Science Inoue Prize for Science, Japan
- 2008/01 - Asahi Newspeper Co. Asahi Award, Asahi Newspaper Co., Japan
- 2007/11 - German Cancer Research Center (DKFZ) Meyenburg Foundation Award 2007
- 2007/11 - Twenty-Fifth Osaka Science Prize, Japan
- 2007/04 - Nikkei Business Publications, Inc. Nikkei BP Technology Award, Nikkei Business Publications, Inc., Japan
- 2007/03 - Japan Society for the Promotion of Science JSPS Prize
- 2006/12 - National Institute of Science and Technology Policy Selected as the Nice-Step researcher by National Institute of Science and Technology Policy (NISTEP), Japan
- 2004/04 - Tokyo Techno Forum 21 Gold Medal, Tokyo Techno Forum 21, Japan
- 2003/07 - Nara Institute of Science and Technology NAIST Award, Nara Institute of Science and Technology, Japan