Photographers at the Gemelli hospital saw two cars escorted by Vatican security leave via a side entrance shortly before 11.00 am (0900 GMT) after staff had put a wheelchair in the trunk of one of the vehicles.
The first of the two cars had darkened windows.
The 84-year-old pope had part of his colon removed on July 4. On Sunday he made his first public appearance since the surgery, standing for about 10 minutes while speaking from the balcony of his suite.