He was born in Paris, the son of Étienne Geoffroy Saint-Hilaire. In his earlier years he showed an aptitude for mathematics, but eventually he devoted himself to the study of natural history and of medicine, and in 1824 he was appointed assistant naturalist to his father. In 1832-1837 he published his great teratological work, Histoire générale et particulière des anomalies de l’organisation chez l’homme et les animaux.
In 1829 he delivered for his father the second part of a course of lectures on ornithology, and during the three following years he taught zoology at the Athne, and teratology at the Ecole pratique. He was elected a member of the French Academy of Sciences in 1833, was in 1837 appointed to act as deputy for his father at the faculty of sciences in Paris, and in the following year was sent to Bordeaux to organize a similar faculty there. He became successively inspector of the academy of Paris (1840), professor of the museum on the retirement of his father (1841), inspector-general of the university (1844), a member of the royal council for public instruction (1845), and on the death of Henri Marie Ducrotay de Blainville, professor of zoology at the faculty of sciences (1850). In 1854 he founded the Acclimatization Society of Paris, of which he was president.
Besides the above-mentioned works, he wrote: Essais de zoologie generale (1841); Vie Etienne Geoffroy Saint-Hilaire (1847); Acclimatation et domestication des animaux utiles (1849); Lettres sur les substances alimentaires et particulièrement sur la viande de cheval (1856); and Histoire naturelle générale des règnes organiques (3 vols., 1854-1862), which was not quite completed. He was the author also of various papers on zoology, comparative anatomy and palaeontology.