Cavendish had won the first two stages of the race, only to be blocked out in yesterday's third stage where he finished fifth.
"He has some sort of lung infection," said team director Tristan Hoffman to cyclingnews.com. "He started to get sick before he came [to Missouri], but it's gotten worse as the days have gone on."
Cavendish has been advised to rest before flying home and has been sent to Kansas City where the race ends on Sunday when he is expected to fly home with his team mates.