Nirvana originally wanted Kevin Kerslake, who had directed the videos for the band's singles "Come as You Are", "Lithium", "In Bloom", and "Sliver", to direct the "Heart-Shaped Box" music video. Kerslake prepared five treatments during July and August 1993, but no shoot arrangements were made and by the end of the month, the group decided to work with Dutch photographer and video director Anton Corbijn. Corbijn, who typically created his own ideas for videos, was initially unsure of directing the video since Cobain's treatment was so detailed. Corbijn said, "But then I looked at it and I thought that actually it was pretty good. I was very amazed by somebody writing a song and having those ideas as precise as he did."
The video begins and ends with the band in a hospital setting watching an old man being administered medication through an IV drip. The majority of the video takes place in a surreal outdoor setting that incorporates imagery from the film The Wizard of Oz. During the song's first verse, the old man from the hospital climbs onto a crow-ridden Christian cross. The second verse introduces a young girl in a Ku Klux Klan costume reaching for human fetuses in a tree, and an overweight woman in a suit with human organs painted onto it and with angel wings affixed to her back. In the video's final cut, the band is only shown performing in the outdoor setting during the choruses, where Cobain's face moves in and out of focus in the camera.While most of the video was devised by Cobain, Corbijn added elements such as the intentionally artificial crows, a ladder for the old man to climb onto the cross with, and a box with a heart at the top that the band performs inside of during the song's final chorus. Corbijn created another cut of the video featuring alternate footage during the final verse, including more shots of the young girl and the woman, and scenes of Cobain lying on his back in the poppy field, with mist surrounding him. This version of the video is featured on the DVD The Work of Director Anton Corbijn.
After the video's release, Kevin Kerslake sued Nirvana, alleging copyright infringement. The case was settled out of court.The video won two MTV Video Music Awards in 1994, for Best Alternative Video and for Best Art Direction. As the ceremony was held after Kurt Cobain's April 1994 death, the awards were accepted by Cobain's former bandmates Novoselic, Grohl, and touring guitarist Pat Smear. "Heart-Shaped Box" also topped the music video category in the 1993 Village Voice Pazz & Jop critics' poll.