Capilouto is a native of Alabama. He received most of his education there and has spent much of his career within the state. He is married to Mary Lynne Capilouto, who is also a dentist and former dean of the School of Dentistry at UAB. The couple have one daughter, Emily.
Capilouto obtained his bachelor's degree from the University of Alabama. His Doctor of Dental Medicine and master's degrees in epidemiology came from UAB. In 1991, he received a doctorate in health policy and management from Harvard School of Public Health. He first joined the UAB faculty in 1975. He served as Dean of the UAB School of Public Health from 1994-2001 before he returned to his research and faculty appointment as professor. He subsequently was named Acting Provost in 2002, assuming the post permanently in 2005. On 4 May 2011, Capilouto was selected to succeed Lee Todd, Jr., the eleventh president of the University of Kentucky. He was hired under a five-year contract with a base annual salary of $500,000 plus $125,000 in benefits and a possible bonus of up to $50,000.