A method and apparatus pertaining to annotating a document window on a display device of a computer-based system. An annotation window is displayed over a selected portion of the document window where the annotation window is defined by a transparent window area bounded by a border. The annotation window enables the selected portion of the document window to be visible through the annotation window. Annotations are displayed within the annotation window where the annotations have a transparent background enabling the selected portion of the document windows to be visible through the transparent background of the annotations. When the annotation window is closed, the annotations are embedded into a contained document shown in the document window so that the annotations and the document are visible simultaneously in the selected portion of the document window.