The Institute of Pathology, University of Debrecen was founded in 1918 as the Department of Pathology, Faculty of Medicine of Count István Tisza University. Pathology education started in the academic year 1921-22. Although the construction work for the new university began in March 1914, the existing pathology building was completed by May 1926.

Professor Ferenc Orsós was the first director of the institute until 1936. He has held several university functions, he was the dean of the Faculty of Medicine and for a year the rector of the university. He founded the Institute of Forensic Medicine in Debrecen. Shortly after his departure, László Jankovich, professor of the Institute of Anatomy, was entrusted by the management of the university for a short period of time. Ödön Borsos-Nachtnebel followed him from 1936 until 1944. In addition to directing the institute, he also participated in the management of the medical faculty as a dean, and was the vice president of the Hungarian Society of Pathology.

Between 1945 and 1947, the activities of the institute were confined to the most necessary routine and educational tasks. Professor Kálmán Sántha was commissioned by the faculty to supervise the institute. The post-war reorganization was carried out by Professor Béla Kellner, a new institute director appointed in 1947. He worked as a dean for a year and started a cancer pathology school in Debrecen, which he completed at the National Institute of Oncopathology in Budapest.

In 1954, Professor Endes Pongrác was appointed director of the institute, who held this position for 24 years. Summarizing his work, he was a prominent, well-known school-creating professor at the institute, who significantly promoted the pathological diagnostics and education in Hungary. His successor was Professor Szabolcs Gomba, who led the institute for 20 years. During this time he promoted the subspecialization of pathology fields and gained the use of modern technology in histological diagnostics. From 1985 for six years, he was also the Deputy Rector of Education at the Medical University of Debrecen. In 1998, his successor became Professor Zoltán Nemes, who took over the management of the institute for nine years. During this period, an aspiration cytology department was established, as well as the foundations of a molecular pathology laboratory. His well-illustrated, bilingual histopathology atlas has been used by students for a long time.

Professor Gábor Méhes (MD, PhD, Doctor of the Hungarian Academy of Sciences) has been the director of the institute since 2007. Using his international experience, the diagnostic workflow and the histological reporting system was reorganized, based on the use of clinical and laboratory IT systems. Advances have been made in the automation of sample processing and staining techniques after the renovation of the laboratories.. The selection of reagents and antibodies suitable for histopathological diagnostics are in line with the latest professional recommendations. High-resolution digitalisation and online examination of the sections are also available. The molecular pathology laboratory has been also expanding. In addition to FISH and PCR-based methods, mutation assays with next-generation sequencing (NGS) are also possible. The infrastructure of the institute is largely determined by the internationally developed technique and work organization of the TIOP renovation completed in 2011. In 2012 a new cytopathology laboratory and an aspiration cytology clinic were established.