Dr. Eric Joel DeMaria, 51, of Tacketts Pond Drive in Raleigh, and John William Cotton, 39, of Loblolly Pine Drive in Raleigh, face embezzlement charges.
DeMaria worked at Duke from July 12, 2005 to August 1, 2010. His last position was physician and director of the bariatric surgery program.
Cotton worked from November 8, 1993 to August 1, 2010. His last position was business manager in the department of surgery.
Both men are free on $25,000 bond.
The warrants say the men took the money between January and the end of December 2009.