| Side With The Seeds | Sky Blue Sky | 165 |
| Shouldn't Be Ashamed | A.M. | 88 |
| Should've Been In Love | A.M. | 74 |
| Should I Stay Or Should I Go? | Cover | 1 |
| She's A Jar | Summerteeth | 319 |
| Shake It Off | Sky Blue Sky | 44 |
| Secret Of The Sea | Mermaid Avenue, Vol. 2 | 21 |
| Screen Door | No Depression | 23 |
| Say You Miss Me | Being There | 47 |
| Save My Ass | | 1 |
| Satan, Your Kingdom Must Come Down | March 16-20, 1992 | 23 |
| Sandusky | March 16-20, 1992 | 2 |
| Sally Free And Easy | Cover | 1 |
| Rock n Roll Queen | | 1 |
| Rock Salt And Nails | Cover | 1 |
| Rising Red Lung | The Whole Love | 21 |
| Ripple | Cover | 5 |
| Retrieval Of You | Down With Wilco | 4 |
| Reservations | Yankee Hotel Foxtrot | 198 |
| Remember The Mountain Bed | Mermaid Avenue, Vol. 2 | 154 |
| Reincarnation | Cover | 20 |
| Reflections On A Crystal Wind | Cover | 4 |
| Red-Eyed And Blue | Being There | 392 |
| Rainbow Connection | Cover | 1 |
| Radio King | Down By The Old Mainstream | 26 |
| Radio Cure | Yankee Hotel Foxtrot | 139 |
| Psycho Killer | Cover | 1 |
| Promising | Chelsea Walls | 9 |
| Pot Kettle Black | Yankee Hotel Foxtrot | 196 |
| Poor Places | Yankee Hotel Foxtrot | 329 |
| Political Science | Cover | 22 |
| Please Tell My Brother | Weird Tales | 53 |
| Please Be Patient With Me | Sky Blue Sky | 13 |
| Piss It Away | | 2 |
| Pink Moon | Cover | 1 |
| Pieholden Suite | Summerteeth | 24 |
| Pick Up The Change | A.M. | 130 |
| Person I Used To Be | | 1 |
| Pecan Pie | Down By The Old Mainstream | 53 |
| Peace In The Valley | | 1 |
| Passenger Side | A.M. | 406 |
| Paranoid | Cover | 2 |
| Panthers (Proving Death Again) | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 2 |
| Outtro | | 1 |
| Outtasite (Outta Mind) | Being There | 426 |
| Outta Mind (Outta Sight) | Being There | 93 |
| Out On The Weekend | Cover | 1 |
| Open Mind | The Whole Love | 11 |
| One Wing | Wilco (the album) | 159 |
| One Sunday Morning (Song For Jane Smiley's Boyfriend) | The Whole Love | 75 |
| One More Night | | 1 |
| One Hundred Years From Now | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 2 |
| One By One | Mermaid Avenue | 120 |
| On And On And On | Sky Blue Sky | 41 |
| Old Maid | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 2 |
| Oklahoma USA | Cover | 6 |
| Nothing'severgonnastandinmyway(again) | Summerteeth | 87 |
| Not For The Season | | 149 |
| No Sense In Lovin' | Anodyne | 24 |
| No Romance | | 1 |
| No More Poetry | Alpha Mike Foxtrot: Rare Tracks 1994-2014 | 5 |
| No Matter What | Cover | 1 |
| No Depression | No Depression | 1 |
| No Church Tonight | | 1 |
| New Years Countdown | | 1 |
| New Madrid | Anodyne | 275 |
| My Words | | 3 |
| My Darling | Summerteeth | 45 |
| Muzzle Of Bees | A Ghost Is Born | 260 |
| More Like The Moon | More Like The Moon EP | 8 |
| Monkey Mess | | 6 |
| Monday | Being There | 333 |
| Modern World | | 1 |
| Misunderstood | Being There | 477 |
| Millionaire | | 7 |
| Midnight Special | | 1 |
| Merciful Night | | 2 |
| Mendocino | Cover | 1 |
| Mellow My Mind | | 1 |
| Lyrical Stance | | 4 |
| Love Will Keep Us Together | Cover | 2 |
| Love & Mercy | Cover | 2 |
| Lost Love | Weird Tales | 21 |
| Losing End | | 3 |
| Lookin' For A Love | Cover | 3 |
| Livin' After Midnight | Cover | 1 |
| Listen To Her Heart | Cover | 21 |
| Life Left Him There | Down With Wilco | 4 |
| Lies of the Living Dead | | 3 |
| Let's Not Get Carried Away | Sky Blue Sky Tour EP | 16 |
| Let's Hear It For Rock and Roll | | 18 |
| Less Than You Think | A Ghost Is Born | 62 |
| Leave Me (Like You Found Me) | Sky Blue Sky | 1 |
| Laminated Cat | Loose Fur | 66 |
| Kingsport Town | Cover | 1 |
| Kingpin | Being There | 332 |
| King of Carrot Flowers, Pt. 1 | Cover | 1 |
| Kicking Television | A Ghost Is Born | 55 |
| Kamera | Yankee Hotel Foxtrot | 215 |
| Just Wanted to Thank You | | 2 |