The watchdog group sent its complaints this month. According to the foundation, Swinney has promoted a culture in the program that promotes Christianity and violates constitutional guidelines against publicly funded institutions endorsing religion or engaging in religious exercises
Swinney said he recruits players of all religions to the team and believes prospects and their families deserve to know the type of person a coach is beyond the football field.
"Players of any faith or no faith at all are welcome in our program. All we require in the recruitment of any player is that he must be a great player at his position, meet the academic requirements, and have good character," Swinney said in a statement.
The foundation said in a letter sent by the group's staff attorney Patrick Elliott that Swinney selected James Trapp as team chaplain, which it said violated Clemson's guidelines. Other violations the group cited were Trapp having an office in an athletic building and being given access to the "entire football team in between drills for the purpose of bible study."
The foundation also said Swinney and staff members were coercive when asking the entire team to attend a Fellowship of Christian Athletes breakfast in 2011, taking the team and staff to church services as it says occurred several times or organizing team devotionals.
"The nonreligious and non-Christian student athletes who come through Clemson's football program deserve to have their rights of conscience protected," Elliott wrote.
The university has said it would review the foundation's complaints, but "we believe FFRF is mistaken in its assessment. The Supreme Court has expressly upheld the right of public bodies to employ chaplains and has noted that the use of prayer is not in conflict with the principles of disestablishment and religious freedom."
When asked on a teleconference later Wednesday if he planned changes following the FFRF's contentions, he said no. "We do things, again, the right way and always have, and we'll continue to run the program the way we always have," he said.
The FFRF said Wednesday in its own statement Swinney needs to take responsibility for his conduct and make changes. The foundation said "his religion is not the issue; it is his proselytizing in a public university football program."
Swinney says he tries to set a good example and will continue to live by his faith. He's proud of what Clemson has accomplished since he took over as head coach in 2008. "We win at the highest level and we graduate players who excel on the field and in life because of their time in Death Valley," he said.