The Institute of Molecular Pathogenesis ( IMP ), together with the Institute of Bacterial Infections and Zoonoses, also located in Jena, represents the expertise of the Friedrich Loeffler Institute in the research of bacterial pathogens.

The IMP is tasked with characterising the interaction between bacterial pathogens of animal diseases and zoonoses and their hosts at the molecular level, evaluating the findings with regard to their relevance in the organism as a whole and using this to develop methods for the prophylaxis and control of infections in farm animals.