On 29 July 1693 Wood was condemned and fined in the vice-chancellor's court for certain libels against the late Edward Hyde, 1st Earl of Clarendon. He was punished by being banished from the university until he recanted, the offending pages being burnt. The proceedings were printed in a volume of "Miscellanies", published by Edmund Curll in 1714. Wood was attacked by Bishop Burnet in "A letter to the Bishop of Lichfield and Coventry" (1693), and defended by his nephew Dr Thomas Wood, in a "Vindication of the Historiographer", to which is added the "Historiographer's Answer" (1693), reproduced in the subsequent editions of the "Athenae". The nephew also defended his uncle in "An Appendix to the Life of Bishop Seth Ward", 1697. After a short illness Anthony Wood died, and was buried in the outer chapel of St John Baptist (Merton College), in Oxford, where he had superintended the digging of his own grave only a few days before.