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In 1200, King Philip II issued a diploma "for the security of the scholars of Paris" that made the students subject only to ecclesiastical jurisdiction.  The provost and other officers were forbidden to arrest a student for any offence, unless this was done to hand over the culprit to ecclesiastical authority.  The king's officers could never lay hands on the head of the schools unless they had a mandate from an ecclesiastical authority. This action was motivated at least in part by a violent incident between students and officers outside the city walls at a pub.

In 1215, the Apostolic legate, Robert de Courçon, issued new rules governing who could become a professor.  To teach the arts it was necessary to have reached the age of twenty-one, to have studied these arts at least six years, and to take an engagement as professor for at least two years. For a chair in theology the candidate had to be thirty years of age with eight years of theological studies, of which the last three years were devoted to special courses of lectures in preparation for the mastership. These studies had to be made in the local schools under the direction of a master, for at Paris one was not regarded as a scholar unless he had a particular master. Lastly, purity of morals was as important as reading. The licence was granted, according to custom, gratuitously, without oath or condition. Masters and students were permitted to unite, even by oath, in defence of their rights, when they could not otherwise obtain justice in serious matters. No mention is made either of law or of medicine, probably because these sciences were less prominent.

Priscian's "Grammar", Aristotle's "Dialectics", mathematics, astronomy, music, rhetoric and philosophy were taught in the arts course; to these might be added the Ethics of the Stagyrite and the fourth book of the Topics. But it was forbidden to read the books of Aristotle on Metaphysics and Physics, or abbreviations of them.

In 1229, a denial of justice by the queen led to suspension of the courses. The pope intervened with a Bull that began with lavish praise of the university: "Paris", said Gregory IX, "mother of the sciences, is another Cariath-Sepher, city of letters".  He commissioned the Bishops of Le Mans and Senlis and the Archdeacon of Châlons to negotiate with the French Court for the restoration of the university, but by the end of 1230 they had accomplished nothing. Gregory IX then addressed a Bull of 1231 to the masters and scholars of Paris. Not only did he settle the dispute, he empowered the university to frame statutes concerning the discipline of the schools, the method of instruction, the defence of theses, the costume of the professors, and the obsequies of masters and students (expanding upon Robert de Courçon's statutes).  Most importantly, the pope granted the university the right to suspend its courses, if justice were denied it, until it should receive full satisfaction.

The pope authorized Pierre Le Mangeur to collect a moderate fee for the conferring of the license of professorship. Also, for the first time, the scholars had to pay for their education: two sous weekly, to be deposited in the common fund.