An autonomy protocol was computer programming that granted a hologram the ability to make its own decisions.
The Doctor received autonomy protocols after being activated for the first time on USS Voyager. (VOY: "Flesh and Blood")
In 2377, Seven of Nine overrode his autonomy protocols in the middle of a sentence when he refused to let her go from sickbay. (VOY: "Imperfection")
Later that year, following presumably insubordinate actions, the Doctor suggested Captain Kathryn Janeway could take away his holodeck privileges and autonomy protocols as punishment, in addition to taking away his holoemitter and confining him to the brig. Janeway declined, saying she couldn't punish him for being himself. (VOY: "Flesh and Blood")