In 1678 the university registers which had been in Wood's custody for eighteen years were removed, as it was feared that he would be implicated in the Popish Plot. To relieve himself from suspicion he took the Oath of Supremacy. During this time he had been gradually completing his great work, which was produced by a London publisher in 1691–1692, 2 vols. folio, "Athenae Oxonienses: an Exact History of all the Writers and Bishops who have had their Education in the University of Oxford from 1500 to 1690", to which are added the "Fasti", or "Annals" for the said time. Wood contemplated publishing a third volume of the "Athenae", printed in the Netherlands. The third appeared subsequently as "a new edition, with additions, and a continuation by Philip Bliss" (1813–1820, 4 vols. 4to). The Ecclesiastical History Society proposed to bring out a fourth edition, which stopped at the "Life", ed. by Bliss (1848, 8vo; see Cent. Mag., N.S., xxix. 135, 268). Bliss's interleaved copy is in the Bodleian.