* 2004 – Pearse Prize, Royal Microscopical Society
* 2005 – Emile Chamot Award
* 2006 – Asahi Prize
* 2008 – Nobel Prize in Chemistry
* 2008 – Order of Culture
* 2008 – Person of Cultural Merit
* 2012 – Golden Goose Award
* 2013 – Member of the United States National Academy of Sciences
* 2018 – Junior third rank (posthumous)