Born in Groningen as the son of Dirk Huizinga, a professor of physiology, and Jacoba Tonkens, who died two years after his birth, he started out as a student of Indo-Germanic languages, earning his degree in 1895. He then studied comparative linguistics, gaining a good command of Sanskrit. He wrote his doctoral thesis on the role of the jester in Indian drama in 1897.
It was not until 1902 that his interest turned towards medieval and Renaissance history. He continued teaching as an Orientalist until he became a Professor of General and Dutch History at Groningen University in 1905. In 1915, he was made Professor of General History at Leiden University, a post he held until 1942. That year, he spoke critically of his country's German occupiers, comments that were consistent with his writings about Fascism in the 1930s. From then until his death in 1945, he was held in detention by the Nazis. He died in De Steeg in Gelderland, near Arnhem, just a few weeks before Nazi rule ended, and he lies buried in the graveyard of the Reformed Church at 6 Haarlemmerstraatweg in Oegstgeest.
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