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In 2011, an instrumental cover was used in the Microsoft advertisement "The Kinect Effect", while a version by Sunday Girl was used by Thomson Holidays for a TV advertisement as part of their "Time for a Holiday?" campaign. In the same year, the original version of the song was featured in a commercial for Milk Every Moment.
In 2013, the version by Sunday Girl was also used in a trailer for the ITV series Vera. A piano version by Maxence Cyrin was used in a commercial for AT&T's "It Can Wait" campaign. Another piano cover was used in the commercial "Why Bring a Child into this World?" by Unilever's "Project Sunlight" campaign.
In 2015, an instrumental, chamber music version was used as the sound track in Acura's "Lightning in a bottle" ad for the 2016 Acura ILX. Maxence Cyrin's version appeared in the cinematic promo for Uncharted 4: A Thief's End.
In 2016, the Nada Surf cover was used in Samsung Gear VR TV Commercial, 'Sharing a Virtual World'.
In 2012, the song was used at the end of the episode "Things Just Got Real" of the ABC series The Neighbors. An instrumental lullaby version by Rockabye Baby! appeared in "The Lesson", another episode of Criminal Minds. A cover of the song by Jade Williams was used at the end of the episode "Battle of the Proxies" of the CBS series The Good Wife.
In 2013, it was used in the intro of the Covert Affairs episode "Dead". In the episode "The Return of The Aquabats!" of the television series The Aquabats! Super Show!, one of the main characters, suffering from amnesia, attempts to recall a memory and exactly quotes the first three lines of the song's second verse. The same character also quotes lines from "Gigantic" and "River Euphrates" in the episode.
In 2015, Maxence Cyrin's version appeared at the end of season 1, episode 9 of USA's Mr. Robot, entitled "eps1.8m1rr0r1ng.qt", as a deliberate nod to plot similarities with Fight Club. The second season of the HBO series The Leftovers featured two versions of "Where Is My Mind?" with the original version in episode 2 "A Matter of Geography" and Maxence Cyrin's cover in 3 other episodes. A cover version by Mindy Jones appeared at the end of season 1, episode 9 of the NBC series Blindspot, entitled "Authentic Flirt".
The Toadies covered the song on The Best of Toadies – Live From Paradise.
Trampled By Turtles covered the song in live performances and, in October 2011, they released their version as a single, available for free download on their website. The single is also for sale through digital retailers with proceeds benefiting WhyHunger.
Umphrey's McGee debuted a cover of the song on November 8, 2014, the band's 2000th show, at The Orpheum Theatre in Madison, WI.
White Wives covered the song for their 2011 release Situationist EP.
Locas Electronicas, a project of Locas in Love and Wolke covered the song with German lyrics. The songs of both Locas Electronicas and Wolke are called "Wo ist mein Kopf" ("Where is my head"), although the translation of the songtext slightly differs.
End of Fashion have been criticised for their uncredited copying of the guitar riff from the "Where Is My Mind?", for their song "O Yeah". For example, Rockus Online Magazine reviewer Jonathon Miller called the song "disturbingly Pixies-ish" and went on to write:
"End of Fashion are having no problem appealing to the 95% of people that haven't heard (and still remember) the Pixies' "Where Is My Mind?" and have never experienced a truly exciting live show, and if that's what the band is aiming for, then they are a complete success."