Three of sixteen JU faculties – the faculties of medicine, pharmacy, and health sciences – together form the Medical College. The Faculty of Medicine is Poland’s oldest unit that educates physicians and was one of the first three faculties of the Studium Generale instituted in 1364. Initially, the faculty was represented by two professors: one for medicine and one for astronomy, and the lectures were held in the Royal Castle on Wawel Hill. In 1400, King Władysław Jagiełło restored the with resources from jewels donated by his late wife, Queen Jadwiga. Among the professors at the time was Jan Kro of Chociebuż, the first physician to be elected rector of the Academy in 1419, and Jan of Pawia, the author of the Statute of the Faculty of Medicine drawn up in 1433. In the 15th century, every physician who practiced in Kraków was obliged to teach medicine, resulting in nearly 50 lectors in medicinis, i.e. teaching members at the Faculty of Medicine. In the 16th century, the Faculty of Medicine had Maciej of Miechów in its ranks, an eminent figure in the history of Polish medicine, a physician and historian known as the Polish Hippocrates, who served as Rector of the University for eight terms.

One of the students of the Kraków university in that period was Wojciech Oczko, who later became the court physician for the Polish royalty and authored the treatise entitled Cieplice (Hot Springs), marking the beginning of Polish balneology, and Przymiot (Attribute), the first monograph on syphilis. Józef Struś, a graduate of the Faculty of Liberal Arts of the JU, doctor, and professor of medicine at the University of Padua, contributed to the development of European medicine with the first modern lecture on the pulse: Sphygmicae artis libri quinque. Sebastian Petrarcy of Pilzno, a physician and philosopher, translator of Aristotle’s works, and a renowned philanthropist gave lectures on how to save human life and health. The 17th century saw a slow decline of the University’s greatness, and the next century, known as the Age of Enlightenment, coincided with the weakening of the Polish state, leading to a time of stagnation and the subsequent collapse of the Academy and the Faculty of Medicine. The plan to reform and restore the state began to merge with the idea of revitalizing the oldest university in Poland.

The Commission of National Education (est. 1773) adopted an education reform plan put forth by Hugo Kołłątaj. The Krakow Academy, the then Main Crown School, with Kołłątaj as its Rector in the years 1783-1786 were assigned a central role in the plan. Kołłątaj sought after allies and partners among the members of the faculty at the university, to finally place his trust in prof. Andrzej Badurski, who in turn took up the task of restoring the re-established Faculty of Medicine to its former splendour and position. He led to establishing the first medical clinics on the Polish territory; the newly-opened clinics were clinics of internal medicine, surgery and obstetrics. Badurski took on the management of the first of them and entrusted the two latter to the care of Rafał Józef Czerwiakowski, who introduced surgery into the curriculum and was one of the first anatomy professors in Poland to regularly carry out posthumous examinations.

Unfortunately, the rapid decline of the Polish state, coupled with the ongoing wars and partitions hampered Kołłątaj and Badurski’s vast and ambitious plans. Some of their projects never saw the light of day, and other were curbed or changed. In the early 19th century, surgery was taught by Johann Nepomuk Rust (Jan Nepomucen Rust), later professor at the University of Berlin, and one of the founders of the German surgical school. The circle of Kraków anatomists included Alojzy Vetter, a talented researcher and a discoverer of semilunar cardiac valves.

The Faculty of Medicine JU came into bloom once again when Kraków gained political autonomy (1815-1846). Among its most eminent scholars at the time were Józef Brodowicz, specializing in internal medicine, and Ludwik Bierkowski, a surgeon, founder of the Museum of Anatomopathology, and a pioneer in general anaesthesia in Poland, who for nearly 30 years stood at the helm of Krakow surgery. Considerable services to the University were also rendered by Józef Majer, a physiologist and anthropologist, two-time Rector of the JU, and the first president of the Polish Academy of Arts and Sciences (PAU), as well as Fryderyk Skobel, a physician and naturalist, Rector of the JU, who became famous as one of the pioneers of employing microscopic research in theoretical sciences. He also played a key part in the development of modern balneology, and in systematizing medical terminology.

Two first decades following the liquidation of the Free City of Kraków (1846) were the time of Germanization and anti-Polish politics of Vienna towards the University. The Faculty of Medicine at the time was privileged to have in its ranks one of the most notable contemporary physicians – Józef Dietl, professor of internal medicine and a balneologist, who went down in history as the one to exclude bloodletting from medical practice applied therein for 1600 years. This period in the history of the Faculty of Medicine and medicine alike was brimming with a great many other figures who contributed to their development. Among them we find such names as Walery Jaworski, co-originator of European gastrology; Jan Mikulicz Radecki, one of the most notable surgeons of the 19th century, pioneer of endoscopy and gastroscopy, co-founder of world thoracic-surgery; Ludwik Rydygier, professor of surgery at the JU, first in Poland to perform pylorus resection and gastroenterostomy; Alfred Obaliński, head of the Chair and Clinic of Surgery of the JU, author of the first radiogram in Poland; Ludwik Karol Teichman, an outstanding anatomist who fully described the lymphatic system; Alfred Biesiadecki, a spearhead of histopathological imaging of skin, and father of modern dermatology; and finally Napoleon Nikodem Cybulski, who together with Stanisław Sxymonowicz laid experimental foundations of the world endocrinology.

Faculty of Medicine entered the 20th century as a thriving scientific and clinical centre particularly successful on account of its research in normal anatomy led by prof. Kazimierz Kostanecki, and in pathologic anatomy carried out by prof. Tadeusz Browicz and prof. Stanisław Ciechanowski. Prof. Tadeusz Tempka formed the basis of haematological school, while the exquisite surgical traditions were perpetuated by professors Bronisław Kader, Maksymilian Rutkowski and Jan Glatzel. Prof. Jan Miodoński, an otolaryngologist, formed one of the most modern of otolaryngological centres in the contemporary Europe. Physiology of world’s highest standards was practised by prof. Jan Kaulbersz, biochemistry and medical chemistry by prof. Leon Machlewski, histology by prof. Stanisław Maziarski, and pharmacology by prof. Janusz Supniewski. Forensic medicine was favoured with two distinguished professors: Leon Wachholz and Jan Olbrycht. Prof. Aleksander Rosner managed a modern obstetrics and gynaecology clinic. Prof. Jan Piltz founded a modern neuropsychiatric school.

The Jagiellonian University operated uninterruptedly during the WWII offering secret underground education. Studies within the clandestine Faculty of Medicine were organized by prof. Stanisław Maziarski. During the first years after the war, the pre-war traditions were followed. In 1950, pursuant to the decision of the contemporary state authorities, all medical faculties in Poland were separated from their mother universities and gradually transformed into medical academies. That was also the inception of Medical Academy in Kraków. despite all the changes, many buildings of various theoretical and clinical departments were being modernized since the 1950s. The plans of rebuilding and equipping the Clinic of Obstetrics and Gynecology and the Clinic of Otolaryngology, thwarted by the war, were being pressed ahead with. Plans to rebuild and modernize Theatrum Anatomicum were being adopted, and new clinics – III Clinic of Internal Diseases and III Clinic of Surgery – instituted.

Since the early 1960s, intensive design work for construction of a new modern building complex was underway, covering an over 100-hectare area in Prokocim. The then Rector of the Academy, prof. Leon Tochowicz aspired to build a scientific, clinical and teaching centre to meet the demands of a rapidly developing university and a growing number of new medical specializations emerging. The construction work began in 1961 and was crowned in 1965 with the opening of the Institute of Pediatrics, erected mainly with the funds from the Polish diaspora in the USA, and later developed with the financial support from the American government. In the 1970s and 80s student dormitories and a medical library were added on to the complex.

The period between 1965 and 1973 is a time of reform and reorganization of teaching, as well as structural centralization of the departments of Medical Academy. Three new institutes were established at the time: Institutes of paediatrics, microbiology and physiology. In 1985 the Clinical Teaching Unit was transformed into the Institute of Clinical Teaching of the Medical Academy in Kraków. In 1993, when the medical Academy was governed by prof. Andrzej Szczeklik, the Faculty of Medicine was restored to its Alma Mater – Jagiellonian University and together with two other faculties formed the Medical College.