A notepad application enables users to create notes associated with electronic documents. The document, configured for rendering by an eReader browser application, is associated with a table of contents defining a plurality of sections of the document. The notepad application displays a note window associated with a section of the document within a user interface of the browser application. When a user generates a note in connection with the note window by indicating a location within the document, the notepad application adds the note to a note region in a note object that is associated with a section of the document defined by the table of contents. The notepad application then can access the note using the table of contents of the document.