Hektoen International

A Journal of Medical Humanities

Samuel Pepys: Stones and groans


Samuel Pepys (who wrote a famous diary), a man with long curly brown hair and a half sheet of music in his hand turning to face the viewer
Samuel Pepys. Portrait by John Hayls, 1666. National Portrait Gallery, London. Via Wikimedia. Public domain.

I polished up that handle so carefully
That now I am the ruler of the Queen’s Navy
HMS Pinafore, Gilbert and Sullivan



Samuel Pepys (1633–1703) did not polish doorknobs to rise in the world. He was well-connected and soon after graduation from Cambridge University entered the employment of his powerful cousin, Edward Montagu. This cousin had risen to a high position in the Cromwell administration, lived in Whitehall Palace where Oliver Cromwell lived, and maintained there an extensive household. Pepys worked as a residential steward, supervising the staff, ordering clothes for the children, paying bills, and taking care of various other affairs.

When Cromwell died in 1658, most British people seemed to prefer a parliamentary monarchy, and the troops of General George Monk tipped the scales in that direction. Pepys accompanied his cousin on the ship that brought King Charles II from the Netherlands to England. Montagu became Lord Sandwich and was put in charge of the British battle fleet. Samuel Pepys was appointed to the Navy Board and was launched from there into a distinguished administrative career.1


A famous diary

Yet by now, Pepys would be utterly forgotten had he had not kept a diary. This diary covered the years from 1660 to 1670 before he stopped because he thought writing was damaging his eyesight. Pepys wrote in code, combining one of the shorthand systems available at the time with foreign words. He never intended to have this diary made public, and indeed it was not deciphered until the eighteenth century. It covers life during the Restoration period, the wars for supremacy of the seas between England and the Netherlands, the plague of 1665, and the Great Fire of London. It also chronicles the author’s life, marriage, peccadillos, and extramarital affairs.2


Cutting for the stone3-5

Samuel Pepys was born in London in 1633, the fifth of eleven children, of whom only three survived infancy. In his youth he was rarely free from pain, suffering from a form of bladder stone that also afflicted his mother and a brother. Details of his illness are excellently covered by Sir Eric Riches.5 At twenty-four, Pepys opted to have his stone removed surgically (1658). At the time this procedure was risky and painful, usually done in the patient’s kitchen. The patient was immobilized on the table in the lithotomy position by an elaborate system of ligatures and four strongmen holding him down. A silver sound was introduced through the penis into the bladder, and then experienced surgeons removed the stone in as brief a time as one minute.  They made an incision between the penis and the anus, cut down to the bladder, and extracted the stone with pincers, leaving the incision unsutured for fear of it becoming infected. Pepys fully recovered within a month. The stone was about two inches in diameter. Pepys kept it in a special case for which he paid twenty-four shillings and celebrated its removal each year on the date of the surgery. Forty years later the incision broke down or opened up, but he nevertheless lived a long life to the age of 70, free of pain but sterile, perhaps because of the surgery he had undergone.


The bubonic plague of 1665

This was the worst outbreak of plague since the Black Death of 1348, causing London to lose some 15% of its population. The poor suffered most, as they lived in overcrowded tenements, with open drains flowing along the center of the streets, slops thrown out of the houses, the stench overwhelming, the streets muddy and buzzing with flies in summer, and decomposing filth attracting flea-carrying, disease-spreading rats.6

Already in late 1664 there was talk of an impending disaster when a bright comet appeared in the sky.6 A few cases were recorded the next April, and in May the Lord Mayor ordered all householders to clean the streets outside their property. In July, aldermen were instructed to find and punish those failing their duty.

In June 1665, Pepys recalls seeing houses marked with a red cross on the doors, and “Lord have mercy upon us” writ there “which was a sad sight to me… and I was forced to buy some roll-tobacco to smell and chew, which took away the apprehension.”2

By 10 June he noted that the plague had come into the city. Then he had heard that four or five people at Westminster had died, and soon he found “coaches and wagons full of people going into the country.” So many people died in July and August that they could not all be buried on time, the streets became empty of people, shops were closed, and on 25 August, Pepys’ personal physician died of the plague.

In July, King Charles II left for Salisbury and then moved on to Oxford. Pepys relocated to Woolwich but continued to manage the affairs of the Navy.

The Lord Mayor and most city officials stayed at their posts, but the exodus of people from the city continued. Businesses were closed; only a few clergymen, physicians, and apothecaries remained. Decomposing corpses began to be stacked up against the walls of houses. Thinking that bad air was involved in transmission, the authorities ordered giant bonfires to be kept burning night and day. Tobacco was thought to be a prophylactic and it was later said that no London tobacconist had ever died during the epidemic.

Soon the streets were left empty of people, wrote Pepys, except for the dead-carts and the dying victims: “Lord! How empty the streets are and how melancholy, so many poor sick people in the streets full of sores, and so many sad stories overheard as I walk, everybody talking of the the dead… and they tell me that in Westminster there is never a physician, and but one apothecary left, all being dead …2 All trade was stopped and people lost their jobs. Yet as Claire Tomalin comments in her book, the plague year was one of the happiest of Pepys’ life and one of the busiest.3 He worked long hours making money and was given two new appointments: overseeing the feeding of the Navy and the administration of the short-lived British colony at Tangiers.1,3 Plague cases continued to occur sporadically until September 1666, when the Great Fire destroyed much of the City of London, killing the rats and putting an end to the epidemic.



Over the next few decades, Pepys remained an important and efficient civil servant and naval administrator, playing an important role in the Third Anglo-Dutch war and the colony at Tangiers.1,3 He took an interest in books, music, science, and the theater; was a member of Parliament, secretary of several commissions, and president of the Royal Society. After the fall of the Stuarts, he lost his job and was twice briefly imprisoned on suspicion of supporting the fallen dynasty and of corruption, but no charges were brought against him. He moved to the suburbs and died at age seventy in May 1703. After more than 300 years, he is still remembered for his diary, one of the gems of English literature.



  1. Richard Ollard. Pepys: A Biography. Holt, Rinehart and Winston, 1974.
  2. Richard Le Gallienne. Passages from the Diary of Samuel Pepys. Boni and Liveright, 1921.
  3. Claire Tomelin. Samuel Pepys: The Unequalled Self. New York: Alfred A. Knopf, 2002.
  4. The Diary of Samuel Pepys: Bladder and kidney stones. https://pepysdiary.com. Annotations as of 14 Feb 2003.
  5. Eric Riches. “Samuel Pepys and his stones.” Ann Roy Coll Surg 1977; 59:11.
  6. “London in 1665,” in “Great Plague of London.” Wikipedia.



GEORGE DUNEA, MD, Editor-in-Chief


Summer 2022  |  Sections  |  Literary Essays

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