Small animal MRI has become one of the most important tools in biomedical research. The increasing availability of genetically manipulated mice and rats further increases the application of small animal MRI in pharmacological, metabolic, structural, and functional studies. Rodents are small with much faster respiratory (80 – 220 breaths/min for mice, and 70 – 140 breaths/min for rats) and heart rates (400 – 700 beats/min for mice, and 300 – 500 beats/min for rats). The large surface area/weight ratio makes mice and rats susceptible to environment changes. For example, the core temperature of anesthetized mice and rats is easily affected by small changes in ambient temperature. This poses a significant concern for functional, metabolic, and pharmacologic MRI studies using small animals. The fast respiratory rate also imposes significant challenges in small animal MRI if ultra-fast EPI-based sequences are not available to users. In some cases, EPI-based ultra-fast pulse sequences do not produce satisfactory quality images in small animal MRI. The images acquired using spin-echo based sequences are susceptible to physiological motions. When EPI-based sequences are satisfactory, a lengthy acquisition may still be necessary to assess a pharmacological, metabolic, or function MRI studies. Thus, maintaining animal physiology is of paramount significance in the success of preclinical MRI using small animals.In contrast to human subjects, MRI of awake rodents would require physical restraint of the animal. Besides being considered inhumane, the stress of prolonged restraint of the awake rodent would introduce uncertainty into the results (especially in functional studies). Thus, small animal MRI has been performed, almost exclusively, in anesthetized animals. Inhalation anesthetics such as isoflurane has seen increasing use in small animal MRI due to its fast response and recovery. It is the most suitable anesthetics for studies of structure/pathology. When functional MRI (fMRI) is pursued, the impact of anesthetics on the neuromodulation affecting basal cerebral hemodynamics, vascular reactivity and/or cerebral metabolism are common concerns. Inhalation anesthetics such as isoflurane remains the most widely used for induction of anesthesia for fMRI. For maintenance during fMRI data acquisition, various agents have been employed, e.g., isoflurane, medetomidine, and alpha-chloralose.Physical restraint has been widely employed with appropriate anesthesia to minimize confounding artifacts from fast respiratory rate of mice and rats. As single-shot EPI-based sequence is rarely satisfactory in generating high quality and high-resolution images of the small anatomical structures of rodents, the physiological motion is the most challenging obstacles to obtain good quality small animal MRI data. For brain imaging, ear and tooth bars are the most commonly used immobilization device to the head in place during MRI. A mouse head holder used in my lab for the past two decades will be described to demonstrate how to avoid “packing” the head tightly in the probe for lengthy imaging study. In body imaging studies, respiratory gating is essential.The most critical physiological parameters to maintain in small animal MRI is the core temperature of the subject. Most labs now use an MR-compatible feedback temperature control to maintain the core temperature of animals in the magnet. A cold mouse/rat will take longer to return to its normal or the pre-set temperature with the heater. Heating up too fast or a lengthy warming up is an extra stress the animals do not need. Thus, it is important to ensure the maintenance of the animal core temperature before it is connected to the feedback control unit. Despite the close monitoring, a normal physiological respiratory rate is not always maintained. For example, respiratory rates of 40 – 60 breaths/min are not uncommonly reported in mice or rats during MRI studies. In my lab, we only image isoflurane-anesthetized mouse breathing at 100 – 120 breaths/min at 37 °C. An extended period of hypothermia and/or physical restraint tightly “packing” the head/neck/body of the subject in the cradle causes animal stress and potential mortality. The procedures to maintain animal physiology for long MRI acquisition will be discussed.