1665 in science
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- Summer – Isaac Newton graduates from the University of Cambridge which is then closed as a precaution against bubonic plague so he retires to his birthplace at Woolsthorpe-by-Colsterworth to develop his theories on calculus, optics and the law of gravitation.
- April 12 – First recorded victim of the 'Great Plague of London' (1665–66), the last major outbreak of bubonic plague in the British Isles.
- September – Robert Hooke's Micrographia published, first applying the term 'cell' to plant tissue, which he discovered first in cork, then in living organisms, using a microscope.
- Athanasius Kircher in Mundus Subterraneus (publication of which begins in Amsterdam) describes giant bones as those belonging to extinct races of humans.
- January 5 – The Journal des sçavans begins publication in France, the first scientific journal.
- March 6 – The Philosophical Transactions of the Royal Society begins publication in England under the editorship of Henry Oldenburg, the first scientific journal in English.
- May 1 – John Woodward, English naturalist and physician (died 1728)
- approx. date – James Petiver, English naturalist and apothecary (died 1718)
- January 12 – Pierre de Fermat, French mathematician (born 1601)
- November 18 – Blaise Francois Pagan, French military engineer (born 1603)