No mention is made in the decrees of 1252 and 1254 of a faculty of theology, which probably came within the province of the cathedral chapter. The connection between the university and the cathedral was very intimate. Examinations were held and degrees conferred, as we have seen, in the chapel of Santa Barbara; the doctors were admitted to the choir, the canons reciprocally to the university theatres. Pope Innocent IV. had referred in flattering terms to the university at the Council of Lyons in 1245; and in 1255 Alexander IV., in a brief dated from Naples, acclaimed it as one of the four wonders of the world, and gave it his pontifical sanction. Boniface VIII. sent the professors a copy of his decretals, and revised the university statutes. The students were divided into eight sections, according to the part of the Peninsula from which they came, and the heads of these sections elected the rector. The election took place at Martinmas, and the installation on St. Catharine’s Day. The newly elected dignitary was escorted to his house by the students, each section being marshalled behind an ensign consisting of the principal fruit of its country. The rivalries between these different groups generally led to blows, and frequently called for the intervention of the authorities. On such occasions it was the privilege of the rector to defray all damages and fines. But the reign of cakes and ale did not always endure at Salamanca. In 1308 the times were so bad that the stipends of the professors were suppressed, and the university only survived the crisis through the self-sacrifice of the chapter and the intervention of the pope, who devoted a ninth of the tithes of the archbishopric of Santiago to its maintenance.
Subsequent pontiffs continued to exhibit great interest in the now flourishing institution, and to it belonged the honour of terminating, by its decision in favour of Clement VI., the schism which had divided the Christian church. A less honourable incident was the unfavourable decision pronounced by its professors on the great project of Columbus, referred to them by Queen Isabel. This verdict was the more surprising as the university had adopted the Copernican system at a time when it was considered heretical and dangerous.