Molina received more than thirty honorary degrees. 
* Yale University (1997)
* Tufts University (2003)
* Duke University (2009)
* Harvard University (2012)
* Mexican Federal Universities: National of Mexico (1996), Metropolitana (2004), Chapingo (2007), National Polytechnic (2009)
* Mexican State Universities: Hidalgo (2002), State of Mexico (2006), Michoacan (2009), Guadalajara (2010), San Luis Potosí (2011)
* U.S. Universities: Miami (2001), Florida International (2002), Southern Florida (2005), Claremont Graduate (announced 2013)
* U.S. Colleges: Connecticut (1998), Trinity (2001), Washington (2011), Whittier (2012), Williams (2015)
* Canadian Universities: Calgary (1997), Waterloo (2002), British Columbia (2011)
* European Universities: East Anglia (1996), Alfonso X (2009), Complutense of Madrid (2012), Free of Brussels (2010),