Combined magnetic resonance-positron emission tomography (MR-PET), acquired either simultaneously in hybrid scanners or sequentially with standalone machines, offers various applications for preclinical studies. For example, in order to develop new diagnostic tools for translation into the clinic, proof-of-concept studies enable the development and implementation of new hardware components and MRI sequences. New PET tracers and contrast agents can also be applied and cross-validated with either modality. Currently, dual-probes are under development, which synergistically combine the advantages of imaging agents from PET and magnetic resonance imaging. MR-PET is also being implemented more frequently to support the monitoring of preclinical treatment studies for the development of new therapeutic agents and strategies. Further applications of combined MR-PET are multi-modal validation studies of new animal models and analysis of brain function and disease mechanisms, which can be monitored longitudinally.