Nicolas-Théodore de Saussure was born into a wealthy, aristocratic, Genevan family, many of whose members were accomplished in the natural sciences, including botany. He was the second child of Horace-Bénédict de Saussure (1740–1799), who was an eminent geologist, meteorologist, physicist and Alpine explorer, and Albertine-Amélie Boissier (1745–1817). His great uncle, Charles Bonnet, was a famous naturalist whose research included experiments on plant leaves. His grandfather Nicolas de Saussure was a noted agriculturist, for whom Nicolas-Théodore was named. Nicolas-Théodore was called "Théodore" to distinguish him from his grandfather, and he published his professional papers under the name Théodore de Saussure after his father died. (While his father was alive, Théodore's papers were published under the name "de Saussure fils", as was the custom of the day for the sons of scientists having the same surname.)