The “backbone” of the IZKF Münster and main funding format since 1996 are the IZKF Research Projects, an equivalent to the “Sachbeihilfe” funding format offered by the DFG. Likewise, research projects are characterised by a high scientific quality and an innovative research topic. They should be in line with the four research foci of the IZKF Münster, namely "Vascular Diseases", "Inflammation and Infection", "Nervous System Diseases" and "Cell Differentiation, Regeneration and Neoplasia". The research projects are generally funded for three years and are financed with up to 110.000 EUROS per year.

When evaluating the funding applications, special weight is given to the specific preliminary work (publications) of the applicants and successful acquisition of qualified third-party funding. During the application process, the new projects are assigned to a suitable research focus based on the actual composition of topics. Some research topics can be assigned to two different research foci, which promotes networking between the scientists of the respective institutions.