A hierarchical document cross-reference system comprises a document server computer remotely accessible by a user computer. The document server computer includes a database which stores the contents of a first document and a second document. The first document contains one or more segments and the second document contains one or more segments. Each segment is identified by a segment identifier. The document server computer also includes a module executable in the document server computer. The module is configured to receive a request to cross-reference the first document and the second document on a key phrase. The module searches the first document and the second document for the key phrase and identifies the segments in the documents containing the key phrase. The module then displays on the user computer a side-by-side display listing the segment identifiers for the identified segments. The segment identifiers for the identified segments in the first document containing the key phrase are displayed in a first list and the segment identifiers for the identified segments in the second document containing the key phrase are displayed in a second list. The user can subsequently select a segment identifier from each list and submit the segment identifiers for display. The module then displays the contents of each segment, with the key phrase highlighted in a distinct color or by other means.