McCaffery said his son Patrick was in "good spirits" after Wednesday morning's operation.
Doctors will continue with tests in the coming days to determine further treatment for Patrick, who turns 14 on Thursday.
McCaffery flew with the Hawkeyes to Dayton on Monday to prepare for their First Four matchup with fellow No. 11 seed Tennessee. It's the first NCAA tournament appearance in eight seasons for Iowa, which made the field despite losing six of its last seven games.
McCaffery returned to the University of Iowa Hospitals & Clinics to be with his family for Wednesday's procedure.
"The outpouring of support and encouragement Patrick and our family have received this past week has been overwhelming; words cannot express how genuinely thankful we are to everyone who has offered their thoughts and prayers," McCaffery said.
McCaffery, 54, is a Philadelphia native and a former standout at Penn.
He is in his fourth season at Iowa after head coaching stints at Siena and UNC-Greensboro. He also spent 11 seasons as an assistant at Notre Dame, where he met his wife Margaret, a former star basketball player for the Fighting Irish.
The McCaffery have three sons and a daughter.
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