Sparklehorse's first album, Vivadixiesubmarinetransmissionplot (1995), was a modest college radio success. In 1996, while touring Europe with Radiohead shortly after the album's release, Mark Linkous consumed a combination of anti-depressants, valium, alcohol, and heroin in a London hotel room. Unconscious and with his legs pinned beneath him for almost fourteen hours, the resulting potassium build-up caused his heart to stop for several minutes after his body was lifted up. The ensuing surgery almost caused him to lose the use of both legs and left him wheelchair-bound for six months and requiring dialysis for acute kidney failure.
Good Morning Spider (1998) was recorded following this incident. Critics have conjectured that Linkous's brush with death inspired the sombre tone of the album, though Linkous stated that much of the material on GMS had already been written. One song that did result from it is "St. Mary", which is dedicated to the nurses at the eponymous hospital in Paddington where Linkous recuperated.
2001 saw the release of It's a Wonderful Life, featuring appearances by Tom Waits, PJ Harvey, Bob Rupe, Nina Persson and Dave Fridmann. Whereas much of Vivadixie... and Spider were recorded solely by Linkous on his Virginia farm, the new album was a more collaborative work. Linkous expressed his satisfaction with the overall sound of It's a Wonderful Life, which was engineered by Joel Hamilton, while also claiming that he would have preferred to include more experimental and instrumental material.
On September 25, 2006, Sparklehorse released their fourth album, Dreamt for Light Years in the Belly of a Mountain, collaborating with Danger Mouse, Christian Fennesz, and Steven Drozd. This album featured the radio release "Don't Take My Sunshine Away" and a remastered version of "Shade And Honey", which Linkous originally wrote for Alessandro Nivola to sing in the 2003 movie Laurel Canyon, as well as a virtually unchanged re-release of "Morning Hollow," the bonus track from It's a Wonderful Life.
In 2008, Sparklehorse recorded a cover of the song "Jack's Obsession," from Tim Burton's The Nightmare Before Christmas for the official compilation album Nightmare Revisited. In 2009, Sparklehorse teamed up with Danger Mouse and David Lynch in the project Dark Night of the Soul.
In 2009, Linkous teamed up with electronic ambient-music artist Christian Fennesz to create In the Fishtank 15, a wafting album EP of experimentation and dreamy atmospherics. The last four live shows, Linkous did together with Fennesz during a European tour that was held during October 2009.