| 'In spite of dungeon fire and sword': penal days in Clogher | Jefferies, Henry A. | Article in Journal | | 2009 |
| A catalogue of the Bishops of Raphoe to A.D. 1600 | Jefferies, Henry A. | Article in Journal | | 1997 |
| A church 'in decline'? The pre-Reformation Irish church | Jefferies, Henry A. | Article in Journal | | 2006 |
| A new history of Cork | Jefferies, Henry A. | Monograph or Collective Volume | History Press Ireland | 2010 |
| Aislinge Meic Con Glinne - an early medieval ‘vision’ of Cork | Jefferies, Henry A. | Article in Journal | | 2022 |
| Ancient crosses in the Faughan river valley, county Derry | Jefferies, Henry A.Johnson, Ethna | Article in Journal | | 1999 |
| Bishop George Montgomery’s Survey of the parishes of Derry diocese : a complete text from c.1609 | Jefferies, Henry A. | Article in Journal | | 1996 |
| Carnal relations and church courts in Tudor Ireland | Jefferies, Henry | Article in Journal | | 2024 |
| Conversion by coercion? The Reformation in Ireland | Jefferies, Henry A. | Article in Journal | | 2018 |
| Cork : historical perspectives with contributions by Gerard O'Brien and Eilis C. Stack | Jefferies, Henry A. | Monograph or Collective Volume | Four Courts | 2004 |
| Derry diocese on the eve of the plantation | Jefferies, Henry A. | Article in Book | | 1999 |
| Desmond : the early years, and the career of Cormac MacCarthy | Jefferies, Henry A. | Article in Journal | | 1983 |
| Desmond before the Norman invasion : a political study | Jefferies, Henry A. | Article in Journal | | 1984 |
| Diocesan synods and convocations in Armagh on the eve of the Tudor reformations | Jefferies, Henry A. | Article in Journal | | 1995 |
| Dr. George Cromer, Archbishop of Armagh (1521-1543), and Henry VIII's reformation | Jefferies, Henry A. | Article in Book | | 2001 |
| Early churches in the Faughan River valley, County Derry | Jefferies, Henry A.Johnston, Ethna | Article in Book | | 2000 |
| Elizabeth's Reformation in the Irish Pale | Jefferies, Henry A. | Article in Journal | | 2015 |
| Erenaghs and Termonlands : another early seventeenth-century account | Jefferies, Henry A. | Article in Journal | | 2002 |
| Erenaghs in pre-plantation Ulster : an early seventeenth-century account | Jefferies, Henry A. | Article in Journal | | 1999 |
| George Montgomery, first Protestant Bishop of Clogher (1605-1621) | Jefferies, Henry A. | Article in Journal | | 1999 |
| George Montgomery, first Protestant bishop of Derry, Raphoe and Clogher (1605-10) | Jefferies, Henry A. | Article in Book | | 2000 |
| Historic sites and traditions. I. Rev. William Reeves' 'Sites of ancient churches in the county of Armagh - December 1879' | | Article in Journal | | 1996 |
| History of the diocese of Clogher | | Monograph or Collective Volume | Four Courts | 2005 |
| Hugh O'Neill, earl of Tyrone, c.1550-1616 | Jefferies, Henry A. | Article in Book | | 2000 |
| Ireland : religion and piety | Jefferies, Henry A. | Article in Book | | 2003 |
| Kilcreevy - a medieval church site | Jefferies, Henry A. | Article in Journal | | 1998 |
| Men, women, the late medieval Church and religion: evidence from wills from county Dublin | Jefferies, Henry A. | Article in Journal | | 2016 |
| Papal letters and Irish clergy : Clogher before the Reformation | Jefferies, Henry A. | Article in Book | | 2005 |
| Parishes and pastoral care in the early Tudor era | Jefferies, Henry A. | Article in Book | | 2006 |
| Prelude to plantation : Sir Cahir O'Doherty's rebellion in1608 | Jefferies, Henry A. | Article in Journal | | 2009 |
| Priests and prelates of Armagh in the age of reformations, 1518-1558 | Jefferies, Henry A. | Monograph or Collective Volume | Four Courts | 1997 |
| Primate George Dowdall and the Marian restoration | Jefferies, Henry A. | Article in Journal | | 1998 |
| Renewal, Reformation, and ruins | Jefferies, Henry A | Article in Book | | 2012 |
| Review article: 'Revisionism' in Tudor reformation studies | Jefferies, Henry A. | Article in Journal | | 2013 |
| Review article: The English Reformation and the Church of Ireland | Jefferies, Henry | Article in Journal | | 2018 |
| The Armagh registers and the re-interpretation of Irish church history on the eve of the reformations | Jefferies, Henry A. | Article in Journal | | 1999 |
| The church among two nations : Armagh on the eve of the Tudor reformations | Jefferies, Henry A. | Article in Journal | | 1998 |
| The church courts of Armagh on the eve of the Reformation | Jefferies, Henry A. | Article in Journal | | 1993 |
| The church in late medieval County Louth | Jefferies, Henry A | Article in Book | NA | 2023 |
| The Diocese of Dromore on the eve of the Tudor reformation | Jefferies, Henry A. | Article in Book | | 1997 |
| The early penal days : Clogher under the administration of Hugh MacMahon, (1701-1715) | Jefferies, Henry A. | Article in Book | | 2005 |
| The early Tudor Reformations in the Irish Pale | Jefferies, Henry A. | Article in Journal | | 2001 |
| The English reformation in Dublin | Jefferies, Henry A. | Article in Journal | | 2016 |
| The founding of Anglo-Norman Cork 1177-85 | Jefferies, Henry A. | Article in Journal | | 1986 |
| The history and topography of Viking Cork | Jefferies, Henry A. | Article in Journal | | 1985 |
| The Irish church and the Tudor reformations | Jefferies, Henry A. | Monograph or Collective Volume | Four Courts | 2010 |
| The Irish parliament of 1560 : the Anglican reforms authorised | Jefferies, Henry A. | Article in Journal | | 1988 |
| The Kildare Revolt : accident of design? | Jefferies, Henry A. | Article in Journal | | 2004 |
| The Kildare revolt : accident or design? | Jefferies, Henry A. | Article in Journal | | 2004 |
| The Madonna of Lettershendony, Co. Derry | Jefferies, Henry A. | Article in Journal | | 1997 |
| The Marian Restoration in Ireland | Jefferies, Henry A. | Article in Journal | | 2016 |
| The parish church and priests of Loughgall, Armagh, in 1546 | Jefferies, Henry A. | Article in Journal | | 1998 |
| The Reformation in Ireland: interpretations old and new | Jefferies, Henry A. | Article in Journal | | 2016 |
| The role of the laity in the parishes of Armagh inter Anglicos, 1518-53 | Jefferies, Henry A. | Article in Journal | | 1998 |
| The secular clergy of the archdiocese of Armagh, 1518-58 | Jefferies, Henry Allen | Thesis | | 1996 |
| The Visions of Mac Conglinne, and their authors | Jefferies, Henry A. | Article in Journal | | 1995 |
| The visitation of the parishes of Armagh 'inter Hibernicos' in 1546 | Jefferies, Henry A. | Article in Book | | 2000 |
| Thr Reformation in Ireland and England: changing stories | Jefferies, Henry A. | Article in Journal | | 2017 |
| Tudor Reformations compared : the Irish Pale and Lancashire | Jefferies, Henry A. | Article in Book | | 2016 |
| Tudor reformations in Cork | Jefferies, Henry A. | Article in Book | | 2016 |
| Tyrone : history and society | | Monograph or Collective Volume | Geography Publications | 2000 |
| Viking Cork | Jefferies, Henry A. | Article in Journal | | 2010 |
| Why the Reformation failed in Ireland | Jefferies, Henry A. | Article in Journal | | 2016 |
| Winners and losers : Bishop George Montgomery and Sir Cathair O'Doherty | Jefferies, Henry A. | Article in Book | | 2010 |
| Women and the Reformation in Tudor Ireland | Jefferies, Henry A. | Article in Journal | | 2022 |