This article represents a first effort at characterizing the theological and interpretive functions of biblical annotations in modern Roman Catholic and Protestant Bibles. It argues that annotations are not simply subservient to their texts, but typically express a theological agenda. This became clear in the battle over annotations among Protestants and between Protestants and Catholics during the 16th and 17th centuries. It is also evident in the present examination of both Bishop Richard Challoner’s annotations (1750) to the English-language Catholic Bible and the notes in the Scofield Reference Bible (1909). The article concludes with a discussion of five basic functions that biblical annotations serve.