The Department of Cell Biology was officially established on April 1, 1979 at the Jagiellonian University Institute of Molecular Biology. Prof. dr hab. Włodzimierz Korohoda became head of the newly founded unit. 
In the 1980s and the 1990s the Department established and developed ties with scientific centres in Germany, the United Kingdom and the USA. This cooperation involved the visits of a number of eminent foreign scholars, including K.E. Wohlfarth-Bottermann, A. Giese, A. Curtis, J. Bereiter-Hahn, L. Wolpert, P. Knauff, and A. Lev. On the other hand, new opportunities opened to the Department staff members, many of whom went to study, teach, and do research abroad.
The Institute started to combine pure research with seeking its potential medical applications and for this purpose it started collaboration with clinical institutions. One of the major fields of this cooperation was the use of cell cultures in the treatment of burns and other specific kinds of wounds. 
Since 2006 the Department has been run by Prof. dr hab. Zbigniew Madeja. It cooperates with many foreign scientific institutions, some of which are now headed by its former staff members, as well as with other research centres in Poland. 
The Department is equipped with the essential scientific apparatus that enables its staff to carry out fruitful research, the findings of which are published in prestigious international journals included in the ISE Master Journal List. In Autumn 2010 the section of Cell and Tissue Engineering was established within the Department. The new unit has received accreditation.