1975 Old Fashioned Love (Takoma)
Christmas with John Fahey Vol. II (Takoma)
1979 John Fahey Visits Washington D.C. (Takoma)
1980 Yes! Jesus Loves Me (Takoma)
1982 Christmas Guitar Volume I (The New Possibility rerecorded)
1983 Railroad (Takoma)
Popular Songs of Christmas & New Year's (Varrick )
1984 Let Go (Varrick)
1985 Rain Forests, Oceans and Other Themes (Varrick)
1986 Christmas Guitar (Varrick )
1987 I Remember Blind Joe Death (Varrick)
1989 God, Time and Causality (Shanachie)
1991 The John Fahey Christmas Album
1992 Old Girlfriends and Other Horrible Memories (Varrick)
1996 Double 78
1997 City of Refuge (Tim/Kerr Records)
The Mill Pond (Double EP) (Little Brother Records)
Womblife (Table of the Elements )
The Epiphany of Glenn Jones (Thirsty Ear Records)
2000 Hitomi (LivHouse Records)
2002 John Fahey Trio, Vol. 1 (Jazzoo Records)
2003 Red Cross (Revenant)
Live albums:
1981 Live in Tasmania (Takoma)
1998 Georgia Stomps, Atlanta Struts and Other Contemporary Dance Favorites (Table of the Elements)
2003 Hard Time Empty Bottle Blues (Table of the Elements)
2004 The Great Santa Barbara Oil Slick (Water/Revenant)
2005 On Air (Tradition & Moderne)
Some Summer Day (Intergroove)