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He studied medicine at the University of Paris under Jean-Étienne Dominique Esquirol (1772–1840), and while a student worked as an intern at the Charenton mental institution. In 1840 he accepted a position at the Salpêtrière, and soon after became director of a mental asylum in Ivry. With Jacques-Joseph Moreau (1804–1884) and others, he founded the influential Annales médico-psychologiques (Medical-Psychological Annals).
In 1840 Baillarger was the first physician to discover that the cerebral cortex was divided into six layers of alternate white and grey laminae. His name is associated with the inner and outer bands of Baillarger, which are two layers of white fibers of the cerebral cortex. The outer band of Baillarger is sometimes referred to as the band of Gennari.
In the field of psychiatry, Baillarger did research on the involuntary nature of hallucinations and the dynamics of the hypnagogic state (the intermediary stage between sleep and wakefulness). In 1854 he provided a description of a bipolar disorder that he referred to as folie à double forme (dual-form insanity). Unbeknownst to him at the time, another French psychiatrist, Jean-Pierre Falret had described the same condition in an article prior to Baillarger's findings. Falret referred to the disorder as folie circulaire (circular madness).
- Recherches sur la structure de la couche corticale des circonvolutions du cerveau, (1840)
- Des hallucinations, des causes qui les produisent et des maladies caractérisent, Mémoires de l’Académie de médecine (1842)
- Hallucinations, Annales médico-psychologiques du système nerveux, (1844)
- Folie à double forme, Annales médico-psychologiques du système nerveux, (1854)
- Recherches sur les maladies mentales, 2 volumes; (1890)
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