| A horizontal - wheeled watermill at Crushyriree, Co. Cork | Cotter, Eamonn | Article in Journal | | 2003 |
| Architectural change and the parish church in post-reformation Cork | Cotter, Eamonn | Article in Book | | 2006 |
| Buttevant : a medieval Anglo-French town in Ireland | Cotter, Eamonn | Monograph or Collective Volume | The author | 2013 |
| Buttevant's not-so-hidden history: the town's medieval defences revealed | Cotter, EamonnLong, PatriciaO'Connor, John | Article in Book | | 2016 |
| Dún na Séad Castle: an early 17th century house at Baltimore, Co. Cork | Cotter, Eamonn | Article in Journal | | 2010 |
| Heritage castles of County Cork | Cotter, Eamonn | Monograph or Collective Volume | Heritage Unit of Cork County Council | 2017 |
| Kilcoe Castle: excavation of a late medieval stronghold in County Cork | Cotter, Eamonn | Article in Journal | | 2012 |
| Late medieval timber from Doneraile | Cotter, EamonnEgan, Ursula | Article in Journal | | 1997 |
| The archaeology of medieval Buttevant | Cotter, Eamonn | Article in Book | | 2013 |
| The archaeology of the Irish Hospitaller preceptories of Mourneabbey and Hospital in context | Cotter, Eamonn | Article in Book | | 2015 |
| The medieval church at Ballyroe, Co. Cork | Cotter, Eamonn | Article in Journal | | 2002 |
| The medieval church at Kilquane, Mourneabbey | Cotter, Eamonn | Article in Journal | | 1995 |
| The medieval moated site at Ballinvinny South, Co. Cork | Cotter, Eamonn | Article in Book | | 2009 |
| The military monks at Mourneabbey | Cotter, Eamonn | Article in Journal | | 2012 |