| | | |
| 1 2 3 | Nomads Indians Saints | | 1990 |
| 1 2 3 | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| 1 2 3 | Live: Back on the Bus, Y'all | | 1991 |
| 1 2 3 [Studio Version] | Live: Back on the Bus, Y'all | | 1991 |
| Airplane | Rites of Passage | | 1992 |
| Airplane | Indigo Girls/Rites of Passage | | 2008 |
| All Along the Watchtower | Live: Back on the Bus, Y'all | | 1991 |
| All That We Let In | All That We Let In | | 2004 |
| All the Way | Despite Our Differences | | 2006 |
| Andy | Come on Now Social | | 1999 |
| Become You | Become You | | 2002 |
| Bitterroot | Become You | | 2002 |
| Blood and Fire | Indigo Girls | | 1989 |
| Blood and Fire | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Blood and Fire | Indigo Girls/Rites of Passage | | 2008 |
| Burn All the Letters | Shaming of the Sun | | 1997 |
| Cara Mia | Shaming of the Sun | | 1997 |
| Cedar Tree | Rites of Passage | | 1992 |
| Cedar Tree | Indigo Girls/Rites of Passage | | 2008 |
| Center Stage | Indigo Girls | | 1989 |
| Center Stage | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Center Stage | Indigo Girls/Rites of Passage | | 2008 |
| Center Stage [Live][*] | Indigo Girls/Rites of Passage | | 2008 |
| Chickenman | Indigo Girls/Rites of Passage | | 2008 |
| Chicken Man | Rites of Passage | | 1992 |
| Closer to Fine | Indigo Girls |  | 1989 |
| Closer to Fine | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Closer to Fine | Retrospective | | 2000 |
| Closer to Fine | Indigo Girls/Rites of Passage | | 2008 |
| Cold Beer and Remote Control | Come on Now Social | | 1999 |
| Collecting You | Become You | | 2002 |
| Come on Home | All That We Let In | | 2004 |
| Compromise | Come on Now Social | | 1999 |
| Cordova | All That We Let In | | 2004 |
| Crazy Game | Strange Fire | | 1987 |
| Crazy Game | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Crazy Game [Original Single Version][*] | Strange Fire | | 1987 |
| Cut It Out | Shaming of the Sun | | 1997 |
| Dairy Queen | All That We Let In | | 2004 |
| Dead Man's Hill | Swamp Ophelia | | 1994 |
| Deconstruction | Become You | | 2002 |
| Devotion [#] | Retrospective | | 2000 |
| Digging for Your Dream [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Dirt and Dead Ends | Despite Our Differences | | 2006 |
| Don't Give That Girl a Gun | Shaming of the Sun | | 1997 |
| Driver Education [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Everybody's Waiting for Someone to Come Home | Strange Fire | | 1987 |
| Everything in Its Own Time | Shaming of the Sun | | 1997 |
| Fare Thee Well | Swamp Ophelia | | 1994 |
| Fill It Up Again | All That We Let In | | 2004 |
| Fleet of Hope [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Fly Away | Despite Our Differences | | 2006 |
| Free in You | All That We Let In | | 2004 |
| Fugitive | Swamp Ophelia | | 1994 |
| Galileo | Rites of Passage | | 1992 |
| Galileo | Retrospective | | 2000 |
| Galileo | Indigo Girls/Rites of Passage | | 2008 |
| Get Out the Map | Shaming of the Sun | | 1997 |
| Get Out the Map | Retrospective | | 2000 |
| Get Together | Strange Fire | | 1987 |
| Get Together | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Ghost | Rites of Passage | | 1992 |
| Ghost | Retrospective | | 2000 |
| Ghost | Indigo Girls/Rites of Passage | | 2008 |
| Ghost of the Gang [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Go | Come on Now Social | | 1999 |
| Go | Retrospective | | 2000 |
| Gone Again | Come on Now Social | | 1999 |
| Hammer and a Nail | Nomads Indians Saints | | 1990 |
| Hammer and a Nail | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Hand Me Downs | Nomads Indians Saints | | 1990 |
| Hand Me Downs | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Heartache for Everyone | All That We Let In | | 2004 |
| Hey Jesus | Strange Fire | | 1987 |
| Hey Jesus | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Hey Kind Friend | Shaming of the Sun | | 1997 |
| History of Us | Indigo Girls | | 1989 |
| History of Us | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| History of Us | Indigo Girls/Rites of Passage | | 2008 |
| Hope Alone | Become You | | 2002 |
| I'll Change [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| I Believe in Love | Despite Our Differences | | 2006 |
| I Don't Wanna Know | Strange Fire | | 1987 |
| I Don't Wanna Know | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| It's Alright | Shaming of the Sun | | 1997 |
| Joking | Rites of Passage | | 1992 |
| Joking | Indigo Girls/Rites of Passage | | 2008 |
| Jonas & Ezekiel | Indigo Girls/Rites of Passage | | 2008 |
| Jonas and Ezekial | Rites of Passage | | 1992 |
| Keeper of My Heart | Nomads Indians Saints | | 1990 |
| Keeper of My Heart | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Kid Fears | Live: Back on the Bus, Y'all | | 1991 |
| Kid Fears | Indigo Girls | | 1989 |
| Kid Fears | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Kid Fears | Retrospective | | 2000 |
| Kid Fears | Indigo Girls/Rites of Passage | | 2008 |
| Land of Canaan | Strange Fire | | 1987 |
| Land of Canaan | Indigo Girls | | 1989 |
| Land of Canaan | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Land of Canaan | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Land of Canaan | Indigo Girls/Rites of Passage | | 2008 |
| Land of Canaan [Radio Single Remix][*] | Indigo Girls/Rites of Passage | | 2008 |
| Language or the Kiss | Swamp Ophelia | | 1994 |
| Last Tears | Despite Our Differences | | 2006 |
| Lay My Head Down | Despite Our Differences | | 2006 |
| Least Complicated | Swamp Ophelia | | 1994 |
| Least Complicated | Retrospective | | 2000 |
| Leaving [#] | Retrospective | | 2000 |
| Leeds | Shaming of the Sun | | 1997 |
| Left Me a Fool | Live: Back on the Bus, Y'all | | 1991 |
| Left Me a Fool | Strange Fire | | 1987 |
| Left Me a Fool | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Let It Be Me | Rites of Passage | | 1992 |
| Let It Be Me | Indigo Girls/Rites of Passage | | 2008 |
| Little Perennials | Despite Our Differences | | 2006 |
| Love's Recovery | Indigo Girls | | 1989 |
| Love's Recovery | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Love's Recovery | Indigo Girls/Rites of Passage | | 2008 |
| Love of Our Lives [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Love Will Come to You | Rites of Passage | | 1992 |
| Love Will Come to You | Indigo Girls/Rites of Passage | | 2008 |
| Love Will Come to You [Live from Eddie's Attic, Atlanta, GA][*] | Indigo Girls/Rites of Passage | | 2008 |
| Make It Easier | Strange Fire | | 1987 |
| Make It Easier | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Moment of Forgiveness | Become You | | 2002 |
| Money Made You Mean | Despite Our Differences | | 2006 |
| Mystery | Swamp Ophelia | | 1994 |
| Nashville | Rites of Passage | | 1992 |
| Nashville | Indigo Girls/Rites of Passage | | 2008 |
| Nuevas Senoritas | Become You | | 2002 |
| Our Deliverance | Become You | | 2002 |
| Ozilline | Come on Now Social | | 1999 |
| Peace Tonight | Come on Now Social | | 1999 |
| Pendulum Swinger | Despite Our Differences | | 2006 |
| Perfect World | All That We Let In | | 2004 |
| Power of Two | 1200 Curfews | | 1995 |
| Power of Two | Swamp Ophelia | | 1994 |
| Power of Two | Retrospective | | 2000 |
| Prince of Darkness | Indigo Girls | | 1989 |
| Prince of Darkness | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Prince of Darkness | Indigo Girls/Rites of Passage | | 2008 |
| Prince of Darkness | Live: Back on the Bus, Y'all | | 1991 |
| Pushing the Needle Too Far | Nomads Indians Saints | | 1990 |
| Pushing the Needle Too Far | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Reunion | Swamp Ophelia | | 1994 |
| Reunion | Retrospective | | 2000 |
| Rise Up | All That We Let In | | 2004 |
| Rock and Roll Heaven's Gate | Despite Our Differences | | 2006 |
| Romeo and Juliet | Rites of Passage | | 1992 |
| Romeo and Juliet | Indigo Girls/Rites of Passage | | 2008 |
| Run | Despite Our Differences | | 2006 |
| Scooter Boys | Shaming of the Sun | | 1997 |
| Second Time Around [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Secure Yourself | Indigo Girls | | 1989 |
| Secure Yourself | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Secure Yourself | Indigo Girls/Rites of Passage | | 2008 |
| Shame on You | Shaming of the Sun | | 1997 |
| Shame on You | Retrospective | | 2000 |
| She's Saving Me | Become You | | 2002 |
| Shed Your Skin | Shaming of the Sun | | 1997 |
| Sister | Come on Now Social | | 1999 |
| Something Real | All That We Let In | | 2004 |
| Soon Be to Nothing | Come on Now Social | | 1999 |
| Southland in the Springtime | Nomads Indians Saints | | 1990 |
| Southland in the Springtime | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Starkville | Become You | | 2002 |
| Strange Fire | Strange Fire | | 1987 |
| Strange Fire | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Strange Fire | Retrospective | | 2000 |
| Sugar Tongue [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Tether | All That We Let In | | 2004 |
| The Girl with the Weight of the World in Her Hands | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| The Wood Song | Swamp Ophelia | | 1994 |
| This Train Revised | Swamp Ophelia | | 1994 |
| Three County Highway | Despite Our Differences | | 2006 |
| Three Hits | Rites of Passage | | 1992 |
| Three Hits | Retrospective | | 2000 |
| Three Hits | Indigo Girls/Rites of Passage | | 2008 |
| Three Hits [Live from Eddie's Attic, Atlanta, GA][*] | Indigo Girls/Rites of Passage | | 2008 |
| Touch Me Fall | Swamp Ophelia | | 1994 |
| Tried to Be True | Indigo Girls | | 1989 |
| Tried to Be True | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Tried to Be True | Indigo Girls/Rites of Passage | | 2008 |
| Tried to Be True | Live: Back on the Bus, Y'all | | 1991 |
| Trouble | Come on Now Social | | 1999 |
| Trouble | Retrospective | | 2000 |
| True Romantic [Band Version] | Poseidon and the Bitter Bug | | 2009 |
| Virginia Woolf | Rites of Passage | | 1992 |
| Virginia Woolf | Indigo Girls/Rites of Passage | | 2008 |
| Walk Away | Strange Fire | | 1987 |
| Walk Away | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Watershed | Nomads Indians Saints | | 1990 |
| Watershed | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Watershed | Retrospective | | 2000 |
| We Are Together | Come on Now Social | | 1999 |
| Welcome Me | Nomads Indians Saints | | 1990 |
| Welcome Me | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| World Falls | Nomads Indians Saints | | 1990 |
| World Falls | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| Yield | Become You | | 2002 |
| You've Got to Show | Become You | | 2002 |
| You and Me of the 10,000 Wars | Nomads Indians Saints | | 1990 |
| You and Me of the 10,000 Wars | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
| You and Me of the 10,000 Wars | Live: Back on the Bus, Y'all | | 1991 |
| You Left It up to Me | Strange Fire | | 1987 |
| You Left It Up to Me | Indigo Girls/Strange Fire/Nomads Indians Saints | | 1998 |
