The ruined church at the village edge is a Grade II listed building, first listed in 1961 and formerly called The Old Parish Church, but later re-listed under the name The Church of St Mary The Virgin. It was probably built c. 1350. It was built in the Perpendicular style, the fabric being mostly of coarse ironstone rubble with ashlar dressings. William Henry Page, writing in 1908, dated the two-light windows of the belfry, the two-light west window, and the tower arch to the 15th century, and noted that the nave walls are older than the tower. Improvements were made in the early 19th century, with a west gallery added in 1814 and a new east end to the chancel in 1819. By the 1820s the church's seating capacity had become insufficient. Plans to enlarge it came to naught partly as a consequence of the rector falling ill. He died in 1843, and a new rector was appointed, who wanted to relocate the church to the village centre.
The Church today:
In the 1960s the church became a focus of media attention after a widely reported incident of graveyard desecration was followed by a series of similar incidents, both at Clophill and across Britain.
The desecration of St Mary's in 1963 was followed by a spate of similar newspaper reports of "black magic rites" in churches in 1963 and 1964, including reports of a series of desecrations in Lancashire, symbols painted on the porch of a church in Bramber, Sussex, and a pentagram and a sheep's heart pierced with thirteen thorns in St Clement's in Leigh-on-Sea.