Patrick Gallagher, 50, of Queens, pleaded not guilty late Tuesday to grand larceny and possession of stolen property. He was released on $5,000 bail.
Authorities accused Gallagher of stealing nearly three dozen items that had been stored in a Sotheby's warehouse in upper Manhattan since Kennedy's death in 1999. The defendant sold the belongings for $5,000 to pay a debt to a bookie, prosecutors said.
A call to Gallagher's attorney was not immediately returned.
Among the stolen items were rare copies of President Kennedy's inaugural address, a 1963 Father's Day card to the president from his son and a copy of the book "John Brown's Body." The book includes an inscription from Jacqueline Kennedy, dated Christmas 1964, telling her son that it was his father's favorite book.
Also taken were telegrams from Prince Rainier of Monaco, Queen Elizabeth II and two-time Democratic presidential candidate Adlai Stevenson congratulating the Kennedys on the birth of their son.
Sotheby's vice president Diana Phillips said all the items have been recovered.
Gallagher, an employee of Sotheby's for 17 years, was "someone we thought we could trust," she said. He has been suspended pending the outcome of the case.
On July 16, 1999, Kennedy, 38, his wife, Carolyn Bessette Kennedy, 33, and her sister, Lauren Bessette, 34, were killed when a single-engine plane Kennedy was piloting crashed in the ocean near Martha's Vineyard.
Gallagher was ordered to return to court on Friday.
By Tom Hays