The son of farmers, Jean Clair was born in the sixth arrondissement of Paris. He was a student at two secondary schools, the lycée Jacques-Decour and the lycée Carnot, before embarking on a course of post-baccalaureat preparation, the so-called khâgne, at the prestigious lycée Henri-IV in Paris. Then he pursued a degree at the Sorbonne, where he was a student of the art historian, André Chastel, and the philosopher, Jean Grenier. Later, he secured a doctorate in art at the Fogg Art Museum at Harvard University. He was, for a time, involved with the Union of Communist Students.

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