In scientific research activity as well as in education of students, the Department of Archaeology cooperates with the Archaeological Institute of Slovak Academy of Sciences, central Slovak museums and cultural heritage institutions on all levels. Besides inland institutions, department cooperates also with leading foreign universities and academies (Berlin, Bochum, Frankfurt am Main, Göttingen, Heidelberg, Köln, Kraków, Mainz). Independently or in cooperation with other institutions, the department continuously deals with different research projects (APVV, VEGA) and realizes archaeological excavations (Rybník, Santovka, Vráble). They are aimed especially on solving of problems such as relationship between human and nature, settlement structure (centre - periphery), settlement strategy and dynamics in different prehistorical and historical periods, using geographical information systems (GIS), modern searching methods and measurement techniques. This was made possible due to the latest technical equipment owned by the department. Scientific results are significantly accelerated by new Dendrochronological laboratory at Department of Archaeology, which is the only lab of its kind among archaeological institutions in the former Czechoslovakia.
Besides excavations for scientific and documentation purposes, members of the department realize within so called business activities also development-led and rescue excavations.