Template:Songs
| Title | Release date | Peak chart positions | Certifications | Album | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| US | US Alt. | US Main | US Rock | AUS | BEL | CAN | IRE | NLD | NZ | UK | ||||
| "Siva" Hut Recordings · Caroline Records | — | — | — | — | — | — | — | — | — | 45 | — | Gish | ||
| "Tristessa" Sub Pop | 1990-12-XX | — | — | — | — | — | — | — | — | — | — | — | ||
| "I Am One" Hut Recordings · Limited Potential | 1992-08-24 | — | — | — | — | — | — | — | — | — | — | 73 | ||
| "Cherub Rock" Hut Recordings · Virgin | 1993-07-13 | — | 7 | 23 | — | 87 | — | 91 | — | — | 16 | 31 | Siamese Dream | |
| "Today" Hut Recordings · Virgin | 1993-09-30 | — | 4 | 28 | — | 57 | — | 82 | — | — | 27 | 44 | ||
| "Disarm" Hut Recordings · Virgin | 1994-03-22 | — | 8 | 5 | — | 16 | — | 13 | — | — | 29 | 11 | ||
| "Rocket" Hut Recordings · Virgin | 1994-07-XX | — | — | 28 | — | — | — | 29 | — | — | 26 | 89 | ||
| "Bullet with Butterfly Wings" Hut Recordings · Virgin · Delabel | 1995-10-23 | 22 | 2 | 4 | — | 19 | — | 18 | 18 | 9 | 41 | 20 |
| Mellon Collie and the Infinite Sadness |
| "1979" Hut Recordings · Virgin | 1996-01-23 | 12 | 1 | 1 | — | 16 | 21 | 2 | 6 | 29 | 9 | 16 |
| |
| "Zero" Hut Recordings · Virgin | 1996-04-23 | — | 9 | 15 | — | — | — | — | — | — | 3 | — |
| |
| "Tonight, Tonight" Hut Recordings · Virgin | 1996-06-11 | 36 | 5 | 4 | — | 21 | 39 | 32 | 13 | 5 | 2 | 7 |
| |
| "Thirty-Three" Hut Recordings · Virgin | 1996-11-12 | 39 | 2 | 18 | — | 51 | — | 24 | — | 16 | 7 | 21 | ||
| "The End Is the Beginning Is the End" Warner Sunset · Warner Bros. | 1997-06-02 | — | 4 | 12 | — | 10 | 37 | 29 | 7 | 74 | 6 | 10 |
| Batman & Robin |
| "Ava Adore" Hut Recordings · Virgin | 1998-05-18 | 42 | 3 | 8 | — | 19 | — | 16 | 15 | 77 | 5 | 11 | Adore | |
| "Perfect" Hut Recordings · Virgin · EMI | 1998-09-07 | 54 | 3 | 33 | — | 56 | — | 11 | — | — | 18 | 24 | ||
| "The Everlasting Gaze" Virgin | 1999-12-09 | — | 4 | 14 | — | — | — | — | — | — | — | — | Machina/The Machines of God | |
| "Stand Inside Your Love" Hut Recordings · Virgin · EMI | 2000-02-21 | — | 2 | 11 | — | 31 | — | — | 30 | — | 17 | 23 | ||
| "Try, Try, Try" Hut Recordings · Virgin | 2000-09-11 | — | — | — | — | — | — | — | — | — | — | 73 | ||
| "Untitled" Hut Recordings · Self-released · Virgin | 2000-11-29 | — | — | — | — | — | — | — | 46 | — | — | — | Rotten Apples | |
| "Tarantula" Reprise | 2007-05-21 | 54 | 2 | 6 | — | 46 | 14 | 30 | 44 | — | — | 59 | Zeitgeist | |
| "That's the Way (My Love Is)" Martha's Music · Reprise | 2007-09-03 | — | 23 | 32 | — | — | — | — | — | — | — | 94 | ||
| "G.L.O.W." Martha's Music | 2008-11-04 | — | 11 | 25 | — | — | — | 80 | — | — | — | — | Non-album single | |
| "The Celestials" Martha's Music | 2012-06-21 | — | 29 | — | 45 | — | 62 | — | — | — | — | — | Oceania | |
| "Being Beige" Martha's Music · BMG | 2014-10-20 | — | — | — | — | — | — | — | — | — | — | — | Monuments to an Elegy | |
| "One and All" BMG | 2014-11-05 | — | — | 34 | — | — | — | — | — | — | — | — | ||
| "Drum + Fife" BMG · Martha's Music | 2014-11-21 | — | — | — | — | — | — | — | — | — | — | — | ||
| "Run2me" Self-released | 2015-10-22 | — | — | — | — | — | — | — | — | — | — | — | ||
| "Solara" Martha's Music · Napalm | 2018-06-08 | — | — | 26 | 47 | — | — | — | — | — | — | — | Shiny and Oh So Bright - Vol. 1 / LP: No Past. No Future. No Sun. | |
| "Silvery Sometimes (Ghosts)" Napalm | 2018-09-14 | — | 38 | — | — | — | — | — | — | — | — | — | ||
| "Knights of Malta" Napalm | 2018-11-09 | — | — | — | — | — | — | — | — | — | — | — | ||
| "Cyr" Martha's Music · Sumerian | 2020-08-28 | — | 19 | — | — | — | — | — | — | — | — | — | CYR | |
| "Confessions of a Dopamine Addict" Sumerian | 2020-09-25 | — | — | — | — | — | — | — | — | — | — | — | ||
| "Anno Satana" Sumerian | 2020-10-09 | — | — | — | — | — | — | — | — | — | — | — | ||
| "Ramona" Sumerian | 2020-10-30 | — | — | — | — | — | — | — | — | — | — | — | ||
| "Purple Blood" Sumerian | 2020-11-20 | — | — | — | — | — | — | — | — | — | — | — | ||
| "Beguiled" Martha's Music | 2022-09-20 | — | 12 | 7 | — | — | — | — | — | — | — | — | ATUM | |
| "Spellbinding" Martha's Music | 2023-03-28 | — | 16 | — | — | — | — | — | — | — | — | — | ||
| "Empires" Martha's Music | 2023-04-13 | — | — | 24 | — | — | — | — | — | — | — | — | ||
| "Mayonaise" Capitol | 2023-11-12 | — | — | — | — | — | — | — | — | — | — | — | Siamese Dream | |
| "—" denotes a release that did not chart or was not released in that territory. | ||||||||||||||