RN
 Series 1
| Series | Box | Folder | Folder Title | 
| 1 | 1 | 1 | "Always Our Children" (Pastoral Letter), 1997 | 
| 1 | 1 | - | Assignments | 
| 1 | 1 | 2 | Philadelphia Archdiocese, 1968-1985 | 
| 1 | 1 | 3 | Denial of Faculties by Washington Archdiocese, 1979 | 
| 1 | 1 | 4 | Rejection by Brooklyn Diocese, 1984-1985 | 
| 1 | 1 | 5 | Removal from Newark Archdiocese, 1987 | 
| 1 | 1 | 6 | Philippines, 1991 | 
| 1 | 1 | 7 | Rejection by Baltimore Archdiocese, 1992 | 
| 1 | 1 | 8 | Rejections by Fall River (MA) and Charlotte (NC) Dioceses, 1999, 2001 | 
| 1 | 1 | 9 | St. John the Baptist Church, New Freedom, PA, 2002 | 
| 1 | 1 | 10 | London Ministry, 2004-2005 | 
| 1 | 1 | 11 | Association for the Rights of Catholics in the Church, 1989, 1992 | 
RN
 Series 1
| Series | Box | Folder | Folder Title | 
| 1 | 1 | - | Awards | 
| 1 | 1 | 12 | Isaac Hecker Award for Social Justice, 1995 | 
| 1 | 1 | 13 | International Lesbian and Gay Human Rights Commission Award, 1997 | 
| 1 | 1 | 14 | P-FLAG Washington Award, 1998 | 
| 1 | 1 | 15 | Dignity New York Extraordinary Service Award, 1999 | 
| 1 | 1 | 16 | OUT Award, 2000 | 
| 1 | 1 | 17 | Yale Divinity School Alumnal Board Award for Distinction in Ordained Ministry within the Church, 2000 | 
| 1 | 1 | 18 | Call to Action Award, 2001 | 
| 1 | 1 | 19 | Dignity Lifetime Achievement Award, 2001 | 
| 1 | 1 | 20 | Boy Scouts of America Case, 1993 | 
| 1 | 1 | 21 | Catholic Coalition for Gay Civil Rights, 1984-1989 | 
| 1 | 1 | 22 | Catholic Parents Network, 1994-1999 | 
| 1 | 1 | 23 | Catholic Standard and Times Coverage, 1996-1999 | 
| 1 | 1 | 24 | Congregation for the Doctrine of the Faith Inquiry re Joseph Selling, 1999-2001 | 
RN
 Series 1
| Series | Box | Folder | Folder Title | 
| 1 | 2 | 1 | Courage (Catholic homosexual group), 1989-1990 | 
| 1 | 2 | 2 | Diaries, 1977, -1978, 1988, 1992 | 
| 1 | 2 | 3 | Justice for [Incarcerated] Priests and Deacons, 2010-2012 | 
| 1 | 2 | 4 | The Lazarus Project, 1997 | 
| 1 | 2 | 5 | Louvain Sabbatical, 1991-1993 | 
| 1 | 2 | 6 | Military Seminars, 1993 | 
| 1 | 2 | 7 | Pedophilia Crisis-Nugent Press, 2002 | 
| 1 | 2 | 8 | Photographs, 1965-1990, undated | 
| 1 | 2 | 9 | Polish Gay Ministry Trip, 1996-1997 | 
| 1 | 2 | 10 | Publicity, 1965-2006 | 
| 1 | 2 | 11 | Restorative Justice, 2011 | 
| 1 | 2 | 12 | Rome Pilgrimage, 1996-1997 | 
RN
 Series 1
| Series | Box | Folder | Folder Title | 
| 1 | 2 | - | Salvatorians | 
| 1 | 2 | 13 | Anti-Nugent Campaign by Fr. James Buckley, 1981-1985 | 
| 1 | 2 | 14 | Eastern Region, 1979-1997 | 
| 1 | 2 | 15 | General Correspondence, 1984-2008 | 
| 1 | 2 | 16 | Personnel File, 1977-1980, 1997 | 
| 1 | 2 | 17 | Provincial and Gay Ministry, 1976-1998 |