| 1641 Depositions | | Website | Trinity College Dublin. Department of History. | 2009 |
| 1641 Depositions. Volume I: Armagh, TCD, MS 836; Louth, TCD, MS 834; Monaghan, TCD, MS 834 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2014 |
| 1641 Depositions. Volume II : Cavan, TCD, MS 832 & MS 833; Fermanagh, TCD, MS 835 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2014 |
| 1641 Depositions. Volume III : Antrim, TCD, MS 838; Derry, TCD, MS 839; Donegal, TCD, MS, 839; Down, TCD, MS 837; Tyrone, TCD, MS 839 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2014 |
| 1641 Depositions: Volume V - Kildare, TCD, MS 813; Meath, TCD, MS 816 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2019 |
| 1641 Depositions: Volume VI: Laois / Queen's County, TCD, MS 815. Offaly / King's County, TCD, MS 814 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2021 |
| 1641 Depositions: Volume VII: Wexford, TCD, MS 818 & TCD, MS 819 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2024 |
| 1641 Depositions; volume IV; Dublin, TCD, MS 809 & TCD, MS 810, Miscellaneous associated papers, TCD, MS 840 | | Monograph or Collective Volume | Irish Manuscripts Commission | 2017 |
| 1659 and the road to Restoration | Clarke, Aidan | Article in Book | | 1995 |
| 28 November 1634 : a detail of Strafford's administration | Clarke, Aidan | Article in Journal | | 1963 |
| A discourse between two councillors of state, the one of England and the other of Ireland (1642) | | Article in Journal | | 1970 |
| A new history of Ireland, vol iii : bibliographical supplement | Clarke, AidanGillespie, RaymondMcGuire, James | Monograph or Collective Volume | Clarendon Press | 1991 |
| A woeful sinner : John Atherton | Clarke, Aidan | Article in Book | | 2003 |
| Alternative allegiances in early modern Ireland | Clarke, Aidan | Article in Journal | | 1992 |
| Bishop William Bedell (1571-1642) and the Irish Reformation | Clarke, Aidan | Article in Book | | 1989 |
| Colonial identity in early seventeenth-century Ireland | Clarke, Aidan | Article in Book | | 1978 |
| Dónal Cregan : historian | Clarke, Aidan | Article in Book | | 2001 |
| Ireland 1534-1660 | Clarke, Aidan | Article in Book | | 1981 |
| Ireland and the general crisis | Clarke, Aidan | Article in Journal | | 1970 |
| Letterbook of George, 16th Earl of Kildare | | Monograph or Collective Volume | Irish Manuscripts Commission | 2013 |
| Lord Sligo's visit to Mycanae | Clarke, Aidan | Article in Journal | | 2008 |
| Pacification, plantation and the Catholic question | Clarke, AidanEdwards, R. W. D. (Robert Walter Dudley) | Article in Book | | 1976 |
| Patrick Darcy and the constitutional relationship between Ireland and Britain | Clarke, Aidan | Article in Book | | 2000 |
| Prelude to restoration in Ireland : the end of the Commonwealth, 1659-60 | Clarke, Aidan | Monograph or Collective Volume | Cambridge University Press | 1999 |
| Recent works (1977-1982) on early modern British history : a review essay | Clarke, AidanCollinson, PatrickMorrill, John Stephen, 1946-Parker, Geoffrey | Article in Journal | | 1984 |
| Recollections of Sophie O'Brien - Croagh Patrick 1904 | Clarke, Aidan | Article in Journal | | 2006 |
| Robert Dudley Edwards (1909-1988) | Clarke, Aidan | Article in Journal | | 1988 |
| Robin Dudley Edwards (1909-88) | Clarke, Aidan | Article in Journal | | 1988 |
| Selling royal favours, 1624-32 | Clarke, Aidan | Article in Book | | 1976 |
| Sir Piers Crosby, 1590-1646 : Wentworth's "tawney ribbon" | Clarke, Aidan | Article in Journal | | 1988 |
| The '1641 massacres' | Clarke, Aidan | Article in Book | | 2013 |
| The 1641 deposition | Clarke, Aidan | Article in Book | | 1986 |
| The 1641 rebellion and anti-popery in Ireland | Clarke, Aidan | Article in Book | | 1993 |
| The army and politics in Ireland, 1625-30 | Clarke, Aidan | Article in Journal | | 1964 |
| The Atherton file | Clarke, Aidan | Article in Journal | | 1979 |
| The Atherton trial | Clarke, Aidan | Article in Journal | | 1979 |
| The breakdown of authority, 1640-41 | Clarke, Aidan | Article in Book | | 1976 |
| The colonisation of Ulster and the rebellion of 1641 (1603-60) | Clarke, Aidan | Article in Book | | 1967 |
| The commission for the despoiled subject, 1641-7 | Clarke, Aidan | Article in Book | | 2011 |
| The earl of Antrim and the first Bishops' War | Clarke, Aidan | Article in Journal | | 1963 |
| The genesis of the Ulster rising of 1641 | Clarke, Aidan | Article in Book | | 1981 |
| The government of Wentworth, 1632-40 | Clarke, Aidan | Article in Book | | 1976 |
| The Graces, 1625-41 | Clarke, Aidan | Monograph or Collective Volume | | 1968 |
| The history of Poynings' Law, 1615-41 | Clarke, Aidan | Article in Journal | | 1972 |
| The Irish economy, 1600-1660 | Clarke, Aidan | Article in Book | | 1976 |
| The letterbook of Richard Boyle, 1st earl of Cork, 1629-1634. Chatsworth House, Hardwick MS 78 | NA | Monograph or Collective Volume | Irish Manuscripts Commission | 2025 |
| The Old English in Ireland, 1625-42 | Clarke, Aidan | Monograph or Collective Volume | Macgibbon & Kee | 1966 |
| The Old English in Ireland, 1625-42 | Clarke, Aidan | Thesis | | 1959 |
| The plantations of Ulster | Clarke, Aidan | Article in Book | | 1986 |
| The policies of the 'Old English' in parliament, 1640-1 | Clarke, Aidan | Article in Book | | 1965 |
| The policies of the 'Old English' in parliament, 1640-41 | Clarke, Aidan | Article in Book | | 1965 |
| Two notes on the parliament of 1634 | Clarke, AidanFenlon, Dermot | Article in Journal | | 1967 |
| Varieties of uniformity : the first century of the Church of Ireland | Clarke, Aidan | Article in Book | | 1989 |