Aldrin, 86, was visiting the South Pole as part of a tourist group when his condition deteriorated, the company White Desert said in a statement.
He was evacuated on the first available flight out of the South Pole to McMurdo Station, a nearby US research base, under the care of a doctor, and his condition was stable, the company said. McMurdo is on Ross Island, just off the coast of Antarctica.
The company's statement, which was posted on the website of a tourism trade group, did not specify the ailment.
Their moonwalk as part of the Apollo 11 lunar landing was watched by a then-record television audience of 600 million people.
The US National Science Foundation, which manages the US Antarctic Program, said Aldrin would eventually be evacuated to New Zealand.