In the peace of the library of St John's College, Oxford, is a reminder of more chaotic times. A rude cannon ball, some 20cm across, is on display. It was supposedly fired from a Parliamentarian cannon in 1644 and struck the college's gate tower during the siege of the stubbornly Royalist city.

The English Civil War left a deep mark across the country, and while St John's cannon ball is possibly the most obvious symbol of how that conflict reached academe, many other echoes of the conflict linger.

Oxford became the Royalist capital during the war, with Charles I residing in the deanery of Christ Church (pictured above) and his counter-parliament meeting in Convocation House close to the Bodleian. The simple benches on which the Cavalier representatives sat remain in place, surrounded by dark oak panelling and beneath a fan-vaulted ceiling. To this day, the hall has no artificial lighting, but it is still used for university ceremonies such as electing the chancellor.

St John's also has a couple of items linked to the execution of Charles I's archbishop, William Laud, a former president of the college. The relics include a commemorative medal cast from 26 gold coins given by the churchman to a member of the college, John Herne, who accompanied him to the scaffold.

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At Bristol University, the gatehouse of a Royalist fort at the end of Royal Fort Road, is now at the centre of the university campus. Prince Rupert, the city's governor during the Civil War, is reputed to have marched through what is now called Rupert's Gate, on the Royalist surrender. Above the archway is a guestroom.

Elsewhere in Bristol, the Manor Hall student residence on Lower Clifton Hill is on the site of a house that Rupert burnt down during the siege of the city in 1643.

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But, most grisly of all, the head of Oliver Cromwell is buried in a secret location close to a plaque in the antechapel of Sidney Sussex College, Cambridge. The Lord Protector studied for a year at the college in 1616. His body was buried at Westminster Abbey in 1658, but was subsequently exhumed, hanged in its shroud at Tyburn and then the head cut off and displayed outside Westminster Hall for 20 years.

It was later put on public show in London in the 18th century - the college has an original painted sign advertising this - but eventually made its way back to the college, where it has been accorded some dignity.