The audit is one of dozens the IRS is performing as a follow up to a survey of more than 300 colleges and universities that the agency began two years ago.
The survey asked the institutions whether business ventures not closely related to their basic functions were turning a profit. It also had questions about executive compensation.
"We already pay income tax," university spokesman Tom Jackson said.
University officials released a letter regarding the audit in response to an open records request by the an Athens newspaper.
In its survey responses, the university said it received no unrelated business income in 2006 from most operations such as parking, food services and its bookstore.
The university listed five tax-exempt organizations: The UGA Research Foundation, the UGA Athletic Association, the University of Georgia Foundation, the Arch Foundation and the UGA Real Estate Foundation. It listed each as a public charity.
The athletic association runs UGA's intercollegiate athletic program, while the UGA Research Foundation promotes and helps fund research.
The Arch Foundation and the University of Georgia Foundation accept donations and invest the money for scholarships, to pay supplements for faculty and for other academic-related purposes.
The UGA Real Estate Foundation is a nonprofit corporation set up to use private debt-financing to build housing, lab space, parking decks and other buildings, as well as acquire land for future expansion.
Each is classified as a public charity, according to UGA's questionnaire responses.
IRS spokesman Mark Green said disclosure policies prevent him from detailing what triggered the audit.
Jackson said the university is one of several being audited under a national program and that the review does not mean any wrongdoing will be found. He said university officials are cooperating with the IRS.
"People get audited by the IRS all the time," Jackson said.