In its early years, the university had a partly hierarchical, partly cooperative structure, in which the Rector was at the top, while the students had little say and were settled at the bottom. The Magister and Doctors constituted the four faculties and elected the academic officials from amidst their ranks. The students, but also all other Supposita (university members), were divided into four Academic Nations. Their elected board members, mostly graduates themselves, had the right to elect the Rector. He presided over the Consistory which included procurators of each of the nations and the faculty deans, as well as over the University Assembly, in which all university teachers participated. Complaints or appeals against decisions of the faculty by the students had to be brought forward by a Magister or Doctor.thumb|The courtyard (arkadenhof) of the current main building, constructed between 1877 and 1884Being considered a Papal Institution, the university suffered a setback during the Reformation. In addition, epidemics, economic stagnation, and the first Siege of Vienna by Ottoman forces had devastating effects on the city, leading to a sharp decline in enrollment. For Emperor Ferdinand I, this meant that the university should be tied to the church to an even stronger degree, and in 1551 he installed the Jesuit Order there. As time went on, conflicts between the Jesuit school and the university arose. This led Emperor Ferdinand II, in 1623, to pass a law that incorporated the Jesuit College into the university. It was only in the mid-18th century that the Jesuits lost influence over the university and when Empress Maria Theresa ensured that the university went under the control of the monarchy. The university would later focus on the education of physicians and civil servants. Her successor Joseph II continued her reforms and further liberalized the university, abolishing official attire and allowing both Protestants and Jews to enroll by 1782, as well as introducing German as the compulsory language of instruction the year later.
in its early years the university had a partly hierarchical partly cooperative structure in which the rector was at the top while the students had little say and were settled at the bottom the magister and doctors constituted the four faculties and elected the academic officials from amidst their ranks the students but also all other supposita (university members) were divided into four academic nations their elected board members mostly graduates themselves had the right to elect the rector he presided over the consistory which included procurators of each of the nations and the faculty deans as well as over the university assembly in which all university teachers participated complaints or appeals against decisions of the faculty by the students had to be brought for,ward by a magister or doctorthumb|the courtyard (arkadenhof) of the current main building constructed between 1877 and 1884being considered a papal institution the university suffered a setback during the reformation in addition epidemics economic stagnation and the first siege of vienna by ottoman forces had devastating effects on the city l:eading to a sharp decline in enrollment for emperor ferdinand i this meant that the university should be tied to the church to an even stronger degree and in 1551 he installed the jesuit order there as time went on conflicts between the jesuit school and the university arose this led emperor ferdinand ii in 1623 to pass a law that incorporated the jesuit college into the university it was only in the mid-18th century that the jesuits lost influence over the university and when empress maria theresa ensured that the university went under the control of the monarchy the university would later focus on the education of physicians and civil servants her successor joseph ii continued her reforms and further liberalized the university abolishing official attire and allowing! both protestants and jews to enroll by 1782 as well as introducing german as the compulsory language of instruction the year later