Preclinical MR imaging make valuable contributions to improving our understanding of human diseases, ranging from insights into the molecular/cellular underpinnings of a disorder, to structural and functional manifestations, to the development of novel pharmacotherapeutic treatment approaches. However, the use of imaging procedures, such as anesthesia, animal preparation (e.g., fasting, premedication), blood sampling, and contrast agent injections can affect animal physiology, and entails potential health risks. We will discuss the challenges associated with setting up and carrying out preclinical MRI procedures, addressing the protocols related to animal handling, induction and maintenance of anesthesia and physiological monitoring, to maximize efficacious data.