The Holy Roman Emperor claimed his right to the inheritance of the Roman Empire of the West. The age is known as the period of the Investiture Controversy, from the theological, philosophical, legal and political battle as to whether the jurisdiction and the possessions of bishops and monasteries should be reconfirmed by every emperor to each bishop and abbot. It was a crucial moment in the development of European politics and in the definition of the relationships between the State and the Church and was to be of great importance in the birth of the national monarchies in Europe, such as the French and the English ones. During this struggle discussions about Law were fundamental, as was the study of the Code of Justinian I, which represented the last expression of Roman civilisation and the basis of the very notion of empire. At this time Gratian, a Camaldolese monk, made his appearance in Bologna. Although some scholars have questioned his existence, he may be easily identified as a historical figure. He was the author of the Decretum Gratiani, which was the first systematic survey of Canon Law (all the laws which control the definition and organisation of the Church of Rome). In this work he tried to reconcile texis of a varied nature, many of which had different points of view concerning the main questions of the Investiture Controversy. His work has been defined as "concordantia discordantium canonum" (an attempt to reconcile apparently divergent legal theories). Gratian was hardly an "objective" interpreter, but he was consistent and tried to establish a homogeneous corpus.

In 1158 four experts in Law, Bulgarus, Martinus, Iacopus and Hugo of Porta Ravegnana, four doctores believed to be pupils of Irnerius, were invited by the Emperor Frederick Barbarossa to the Diet of Roncaglia to express their "scientific" Empire.Three of them, Martinus being the exception, pronounced themselves in favour of the Empire. They proved through very subtle glossae that the Roman Law entrusted to the Empire was the only valid law.

In 1158, Frederick I Barbarossa issued a Constitutio Habita which established that every school of learning should constitute a societas of socii (pupils), presided over by a dominus (master) who was to be paid with sums of money granted to him the students. The Empire pledged to protect all those scholars who had to travel for their studies from any interference on the part of political authorities. This is an extremely important event in the history of European universities. The university legally became the place where research could be carried out, independent of any other power.

However, Frederick I issued this edict to reward those scholars who had upheld his claims. For the first time Bologna professors were faced with the difficult problem of the relationship between the University and the political power.