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MacQuarrie, Alan; Boardman, Steve and Williamson, Eila, eds. (2010) Scottish saints' legends in the Aberdeen breviary. In: The Cult of Saints and the Virgin Mary in Medieval Scotland. Studies in Celtic History . Boydell & Brewer, Woodbridge, pp. 143-158. ISBN 9781843835622

MacQuarrie, Alan; Maclean, Colin and Veitch, Kenneth, eds. (2006) Early christianity in Scotland : the age of saints. In: Scottish life and society. John Donald, Edinburgh. ISBN 9780859766500

MacQuarrie, Alan; Maclean, Colin and Veitch, Kenneth, eds. (2006) The cult of saints in medieval Scotland. In: Scottish life and society. John Donald, Edinburgh. ISBN 9780859766500

Clackson, Anne and Lindsay, Sheryl and MacQuarrie, Alan (2006) The homes from hell? Media perceptions of residential child care. Scottish Journal of Residential Child Care, 5 (1). ISSN 1478-1840

MacQuarrie, Alan (2004) Medieval Scotland: Kingship and Nation, AD 80-1460. Sutton, Stroud.

MacQuarrie, Alan (2001) The office for St Blane (10 August) in the Aberdeen Breviary. Innes Review, 52 (2). pp. 111-135.

MacQuarrie, Alan (2000) The offices for St Columba (9 June) and St Adomnán (23 September) in the Aberdeen Breviary. Innes Review, 51 (1). pp. 1-39.

MacQuarrie, Alan; Porter, James, ed. (1999) Early christian communities in the north east : the evidence from Deer and from St Laurence's kirk at Conveth. In: After Columba, after Calvin. Elphinstone Institute Occasional Publications . University of Aberdeen, Elphinstone Institute, Aberdeen, pp. 13-18.

MacQuarrie, Alan (1997) The Govan Cross at Jordanhill and at Govan. Annual Report of the Society of Friends of Govan Old, 7. pp. 4-7.

MacQuarrie, Alan (1997) The Saints of Scotland: Essays in Scottish Church History, AD 450-1093. John Donald, Edinburgh. ISBN 085976446X

MacQuarrie, Alan (1997) The name Govan, the Kirk and the Doomster Hill. Annual Report of the Society of Friends of Govan Old, 7. pp. 1-3.

MacQuarrie, Alan (1996) An eleventh-century account of the foundation legend of Laurencekirk, and of Queen Margaret's pilgrimage there. Innes Review, 47 (2). pp. 95-109.

Munro, R.W. and MacQuarrie, Alan (1996) The Clan MacQuarrie: a History. Clan MacQuarrie Association, Auburn, Massachussets.

MacQuarrie, Alan (1996) Lives of Scottish Saints in the Aberdeen Breviary : some problems of sources for Strathclyde Saints. Records of the Scottish Church History Society, 26. pp. 31-54.

MacQuarrie, Alan (1995) Lections for St Constantine's Day (11 March) in the Aberdeen Breviary. Annual Report of the Society of Friends of Govan Old, 5. pp. 25-32.

MacQuarrie, Alan; Ritchie, Anna and Ritchie, Anna, eds. (1994) The historical context of the Govan stones. In: Govan and its early medieval sculpture. Sutton, Stroud, pp. 27-32. ISBN 9780750907170

MacQuarrie, Alan; Philippart, Guy, ed. (1994) Medieval Scotland. In: Hagiographies. Brepols, Turnhout, Belgium, pp. 487-501. ISBN 9782503504087

MacQuarrie, Alan (1994) St Columba and his lay contemporaries in Scotland and Ireland. Records of the Scottish Church History Society, 25. pp. 188-203.

MacQuarrie, Alan (1993) Vita sancti servani : the life of St Serf. Innes Review, 44 (2). pp. 122-152.

MacQuarrie, Alan; Grant, A and Stringer, K J, eds. (1993) The Kings of Strathclyde, c. 400-1018. In: Medieval Scotland. Edinburgh University Press, Edinburgh, pp. 1-19. ISBN 9780748611102

MacQuarrie, Alan; Blair, John and Sharpe, Richard, eds. (1992) Early christian religious houses in Scotland : foundation and function. In: Pastoral care before the parish. Studies in the Early History of Britain . Continuum International Publishing, Leicester, pp. 110-133. ISBN 9780718513726

MacQuarrie, Alan (1990) Early christian Govan : the historical context. Records of the Scottish Church History Society, 24. pp. 1-17.

MacQuarrie, Alan (1987) Kings, Lords, and Abbots : power and patronage at the medieval monastery of Iona. Transactions of the Gaelic Society of Inverness, 54. 355 -375.

MacQuarrie, Alan (1987) The date of St Ninian's mission : a reappraisal. Records of the Scottish Church History Society, 23. pp. 1-25.

MacQuarrie, Alan (1986) The Career of St Kentigern of Glasgow : Vitae, Lectiones, and Glimpses of Fact. Innes Review, 37 (1). pp. 3-24. ISSN 0020-157X

MacQuarrie, Alan (1985) Scotland and the Crusades. John Donald, Edinburgh. ISBN 0859764451

Cowan, I.B. and Mackay, P.H.R. and MacQuarrie, Alan (1983) The Knights of St John of Jerusalem in Scotland. Scottish History Society Fourth Series . Scottish History Society, Edinburgh. ISBN 0906245036

MacQuarrie, Alan (1982) Anselm Adornes of Bruges: Traveller in the East and Friend of James III. Innes Review, 33. pp. 15-22.

MacQuarrie, Alan (1982) The Bethlehemite Hospital of St Germains, East Lothian. Transactions of the East Lothian Antiquarian and Field Naturalists' Society, 17. pp. 1-10.

MacQuarrie, Alan; (1981) The crusades and the Scottish Gaidhealtachd in fact and legend. In: The Middle Ages in the Highlands. Inverness Field Club, Inverness, pp. 130-141. ISBN 0950261211

MacQuarrie, Alan (1981) The ideal of the holy war in Scotland. Innes Review, 32. pp. 83-92. ISSN 0020-157X

MacQuarrie, Alan (1971) Notes on some charters of the Bruces of Annandale. Transactions of the Dumfriesshire and Galloway Natural History and Antiquarian Society, 3 (58). pp. 72-79.