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1975
Hunter, Michael (1975) John Aubrey and the realm of learning. London, UK: Duckworth Overlook. ISBN 9780715608180.
1981
Hunter, Michael (1981) Science and society in restoration England. Cambridge, UK: Cambridge University Press. ISBN 9780521296854.
Hunter, Michael (1981) The Victorian villas of Hackney. London, UK: The Hackney Society. ISBN 9780950655819.
Hunter, Michael (1981) The preconditions of preservation: a historical perspective. In: Lowenthal, D. and Binney, M. (eds.) Our Past Before Us: Why Do We Save It? Chicester, UK: Wiley-Blackwell, pp. 22-32. ISBN 9780851172194.
1985
Hunter, Michael (1985) The problem of "atheism" in early modern England. Transactions of the Royal Historical Society 35 , pp. 135-157. ISSN 0080-4401.
1988
Gregory, Annabel and Hunter, Michael, eds. (1988) An astrological diary of the 17th Century: Samuel Jeake of Rye, 1652-1699. Oxford, UK: Oxford University Press. ISBN 9780198229629.
1989
Hunter, Michael and Schaffer, S., eds. (1989) Robert Hooke: new studies. Martlesham, Suffolk, UK: Boydell & Brewer. ISBN 9780851155234.
1991
Ucko, P.J. and Hunter, Michael and Clark, A.J. and David, A., eds. (1991) Avebury reconsidered: from the 1660s to the 1990s. Unwin Hyman. ISBN 9780044459194.
1992
Hunter, Michael and Wootton, D., eds. (1992) Atheism from the Reformation to the Enlightenment. Oxford, UK: Oxford University Press. ISBN 9780198227366.
1994
Hunter, Michael, ed. (1994) Robert Boyle reconsidered. Cambridge, UK: Cambridge University Press. ISBN 9780521892674.
Hunter, Michael (1994) The Royal Society and its fellows 1660-1700: the morphology of an early scientific institution. London, UK: British Society for the History of Science. ISBN 9780906450093.
1995
Hunter, Michael (1995) Establishing the new science: the experience of the early Royal Society. Martlesham, Suffolk, UK: Boydell & Brewer. ISBN 9780851155067.
Hunter, Michael (1995) How to edit a seventeenth-century manuscript: principles and practice. The Seventeenth Century 10 (2), pp. 277-310. ISSN 0268-117X.
Hunter, Michael (1995) Science and the shape of orthodoxy: intellectual change in late 17th-century Britain. Martlesham, Suffolk, UK: Boydell & Brewer. ISBN 9780851155944.
1996
Hunter, Michael (1996) Preserving the past: the rise of heritage in modern Britain. Stroud, UK: Sutton Publishers. ISBN 9780750909518.
Davis, E.B. and Hunter, Michael, eds. (1996) Robert Boyle: a free enquiry into the vulgarly received notion of nature. Cambridge Texts in the History of Philosophy. Cambridge, UK: Cambridge University Press. ISBN 9780521561006.
1997
Hunter, Michael (1997) Boyle versus the Galenists: a suppressed critique of seventeenth-century medical practice and its significance. Medical History 41 (3), pp. 322-361. ISSN 0025-7273.
1998
Hunter, Michael, ed. (1998) Archives of the scientific revolution: the formation and exchange of ideas in Seventeenth-century Europe. Martlesham, Suffolk, UK: Boydell & Brewer. ISBN 9780851155531.
Hunter, Michael (1998) Witchcraft and the decline of belief. 18th-century Life 22 (2), pp. 139-147. ISSN 0098-2601.
1999
Hunter, Michael (1999) Introduction. [Editorial/Introduction]
Hunter, Michael (1999) Robert Boyle (1627–91): a suitable case for treatment? British Journal for the History of Science 32 (3), pp. 261-275. ISSN 0007-0874.
Hunter, Michael and Mandelbrote, G. and Ovenden, R. and Smith, N., eds. (1999) A radical's books: the library catalogue of Samuel Jeake of Rye, 1623-90. Martlesham, Suffolk, UK: Boydell & Brewer. ISBN 9780859914710.
2000
Hunter, Michael (2000) Robert Boyle (1627-91): scrupulosity and science. Martlesham, Suffolk, UK: Boydell & Brewer. ISBN 9780851157986.
2001
Hunter, Michael (2001) Introduction. In: Hunter, Michael (ed.) The occult laboratory: magic, science and second sight in late 17th century Scotland. Woodbridge, UK: Boydell Press, pp. 1-49. ISBN 9780851158013.
Boyle, R. (2001) The correspondence of Robert Boyle, 1636–1691. The Pickering Masters 1-6. London, UK: Pickering & Chatto Publishers. ISBN 1851961259.
Hunter, Michael, ed. (2001) The occult laboratory: magic, science and second sight in late 17th-century Scotland. Martlesham, Suffolk, UK: Boydell & Brewer. ISBN 9780851158013.
2002
Hunter, Michael (2002) Scientific change: its setting and stimuli. In: Coward, B. (ed.) A Companion to Stuart Britain. Wiley, pp. 214-229. ISBN 9780631218746.
2003
Harris, F. and Hunter, Michael, eds. (2003) John Evelyn and his milieu. London, UK: British Library Publishing. ISBN 9780712348171.
Bennett, J. and Cooper, M. and Hunter, Michael and Jardine, L., eds. (2003) London's Leonardo: the life and work of Robert Hooke. Oxford, UK: Oxford University Press. ISBN 9780198525790.
Hunter, Michael (2003) Whither editing? [Book Review]
January 2004
Hunter, Michael (2004) Robert Hooke revivified. Notes and Records of the Royal Society of London 58 (1), pp. 89-91. ISSN 0035-9149.
2005
Boyle, R. (2005) Robert Boyle's 'heads' and 'inquiries'. Occasional Papers of the Robert Boyle Project 1. London, UK: Robert Boyle Project. ISBN 0955160804.
Hunter, Michael and Money, David (2005) Robert Boyle’s first encomium: two Latin poems by Samuel Collins (1647). The Seventeenth Century 20 (2), pp. 223-241. ISSN 0268-117X.
Boyle, R. (2005) Unpublished material relating to Robert Boyle's 'memoirs for the natural history of human blood'. Occasional Papers of the Robert Boyle Project 2. London, UK: Robert Boyle Project. ISBN 0-9551608-1-2.
22 January 2005
Hunter, Michael (2005) Report. Robert Boyle for the twenty-first century. Notes and Records of the Royal Society 59 (1), pp. 87-90. ISSN 0035-9149.
August 2005
Hunter, Michael (2005) New light on the ‘Drummer of Tedworth’: conflicting narratives of witchcraft in Restoration England. Historical Research 78 (201), pp. 311-353. ISSN 0950-3471.
2006
Hunter, Michael and Cooper, M., eds. (2006) Robert Hooke: tercentennial studies. Abingdon, UK: Routledge. ISBN 9780754653653.
2007
Hunter, Michael and Davis, E.B. and Knight, H. and Littleton, C. and Principe, L.M. (2007) The Boyle papers: understanding the manuscripts of Robert Boyle. Aldershot, UK: Ashgate Publishing. ISBN 9780754655688.
Hunter, Michael (2007) Editing early modern texts: an introduction to principles and practice. Basingstoke, UK: Palgrave Macmillan. ISBN 9780230008076.
Hunter, Michael (2007) Robert Boyle and the early Royal Society: a reciprocal exchange in the making of Baconian science. British Journal for the History of Science 40 (1), pp. 1-23. ISSN 0007-0874.
Knight, H. and Hunter, Michael (2007) Robert Boyle's 'Memoirs for the natural history of human blood' (1684): print, manuscript and the impact of Baconianism in seventeenth-century medical science. Medical History 51 (2), pp. 145-164. ISSN 0025-7273.
2008
Anstey, P. and Hunter, Michael (2008) Robert Boyle's 'Designe about Natural History'. Early Science and Medicine 13 (2), pp. 83-126. ISSN 1383-7427.
Hunter, Michael and Anstey, P. (2008) The text of Robert Boyle's 'Designe about natural history'. Other. Robert Boyle Project, Birkbeck, London, UK.
Boyle, R. (2008) The text of Robert Boyle's 'Designe about natural history’. Occasional Papers of the Robert Boyle Project 3. London, UK: Robert Boyle Project. ISBN 978-0-9551608-2-0.
2009
Hunter, Michael (2009) British printed images to 1700. Art Libraries Journal 34 (2), pp. 4-9. ISSN 0307-4722.
13 September 2009
Hunter, Michael (2009) Boyle: between God and science. New Haven, U.S.: Yale University Press. ISBN 9780300123814.
November 2009
Hunter, Michael (2009) Genius eclipsed: the fate of Robert Boyle. History Today 59 (11), ISSN 0018-2753.
May 2010
Hunter, Michael (2010) Printed images in early modern Britain: essays in interpretation. Farnham, UK: Ashgate. ISBN 9780754666547.
June 2011
Hunter, Michael (2011) The Royal Society and the decline of magic. Notes and Records of the Royal Society of London 65 (2), pp. 103-119. ISSN 0035-9149.
June 2013
Hunter, Michael (2013) Life-writing in early modern England. The Historical Journal 56 (2), pp. 583-592. ISSN 0018-246X.
2015
Hunter, Michael and Boran, E. (2015) Introduction: special issue on Robert Boyle. Intellectual History Review 25 (1), pp. 1-4. ISSN 1749-6977.
Hunter, Michael (2015) Robert Boyle's early intellectual evolution: a reappraisal. Intellectual History Review 25 (1), pp. 5-19. ISSN 1749-6977.
2016
Hunter, Michael (2016) Pitcairneana: an atheist text by Archibald Pitcairne. The Historical Journal 59 (02), pp. 595-621. ISSN 0018-246X.
12 October 2016
Hunter, Michael (2016) John Webster, the Royal Society and the displaying of supposed Witchcraft (1677). Notes and Records: the Royal Society Journal of the History of Science 71 (1), pp. 7-19. ISSN 0035-9149.
2017
Hunter, Michael (2017) Anti-Atheism in Early Modern England 1580–1720: the atheist answered and his error confuted, written by Kenneth Sheppard. [Book Review]