The cover art for Houses of the Holy was inspired by Arthur C. Clarke's novel Childhood's End. The cover is a collage of several photographs which were taken at the Giant's Causeway, Northern Ireland, by Aubrey Powell of Hipgnosis. This location was chosen ahead of an alternative one in Peru which had also been considered.[22]

The photo shoot featured two naked child models, Stefan and Samantha Gates. It was a frustrating affair over the course of 10 days. Shooting was done first thing in the morning and at sunset in order to capture the light at dawn and dusk, but the desired effect was never achieved due to constant rain and clouds. The photos of the two children were taken in black and white and were multi-printed to create the effect of 11 individuals that can be seen on the album cover. The results were unsatisfactory, but some accidental tinting effects in post-production created a suitable cover. The inner gatefold photograph was taken at Dunluce Castle nearby the Causeway.[22] In February 2010, Stefan Gates was featured on a BBC Radio 4 documentary about the cover. He said there was something sinister about the image, though his sister disagreed. He also admitted never having heard the album. The programme ended with Gates returning to Giant's Causeway and listening to the album on a portable player, after which he said that a great weight had been lifted from him.[23] Samantha also appeared on the back cover of the band's 1976 album Presence.