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Van der Waals was born in Leyden, the Netherlands, as the son of Jacobus van der Waals and Elisabeth van den Burg. He became a school teacher, and later was allowed to study at the university, in spite of his lack of classical languages. He studied from 1862 to 1865, earning degrees in mathematics and physics.
In 1866, he became director of a secondary school in The Hague. In 1873, he obtained a doctorate degree.
Van der Waals died in Amsterdam.