Schelling was born in the town of Leonberg in the Duchy of Wurttemberg (now Baden-Wurttemberg), the son of Joseph Friedrich Schelling and his wife Gottliebin Marie. He attended the monastic school at Bebenhausen, near Tubingen, where his father was chaplain and an Orientalist professor. From 1783 to 1784 Schelling attended a Latin school in Nurtingen and knew Friedrich Holderlin, who was five years his senior. On 18 October 1790, at the age of 15, he then was granted permission to enroll at the Tubinger Stift (seminary of the Evangelical-Lutheran Church in Wurttemberg), despite not having yet reached the normal enrollment age of 20. At the Stift, he shared a room with Hegel as well as Holderlin, and the three became good friends.  Schelling studied the Church fathers and ancient Greek philosophers. His interest gradually shifted from Lutheran theology to philosophy. In 1792 he graduated with his master's thesis, titled Antiquissimi de prima malorum humanorum origine philosophematis Genes. III. explicandi tentamen criticum et philosophicum, and in 1795 he finished his doctoral thesis, titled De Marcione Paulinarum epistolarum emendatore (On Marcion as emendator of the Pauline letters) under Gottlob Christian Storr. Meanwhile, he had begun to study Kant and Fichte, who influenced him greatly.  In 1797, while tutoring two youths of an aristocratic family, he visited Leipzig as their escort and had a chance to attend lectures at Leipzig University, where he was fascinated by contemporary physical studies including chemistry and biology. At this time he also visited Dresden, where he saw collections of the Elector of Saxony, to which he referred later in his thinking on art. On a personal level, this Dresden visit of six weeks from August 1797 saw Schelling meet the brothers August Wilhelm Schlegel and Karl Friedrich Schlegel and his future wife Caroline (then married to August Wilhelm), and Novalis.

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He attended the monastic school at Bebenhausen, near Tubingen, where his father was chaplain and an Orientalist professor.