An autograph manuscript is one written in the hand of the author (as opposed to a copyist or secretary).
Sometimes the term is used more loosely: when publishers refer to the manuscripts of twentieth-century authors, they usually mean typescripts, i.e., the author's typed draft from which the typesetters worked. In this sense, a manuscript can be the form of any work not yet printed. In the age of desktop publishing, that distinction will get ever more difficult to preserve.
Note: This guide is still in the early stages of development.
Three question marks mean I have to write more on the subject. Bear with me.