Magnetic Resonance Imaging (MRI) is a safe and widely used diagnostic imaging method that allows in vivo observation of anatomy and characterization of tissues. MRI provides a method to monitor patients without invasive measures, making it suitable for both diagnostics and longitudinal monitoring of various pathologies. A notable example of this is the work carried out by the Alzheimer's Disease Neuroimaging Initiative (ADNI), which utilizes imaging, including multiple MRI techniques, to monitor disease progression in AD patients and evaluates treatment responses and prevention strategies. Similarly, MRI has been extensively used in evaluating diseases in a variety of animal models. In order to detect subtle anatomical changes over time, small differences in MR images must be accurately extracted. Furthermore, to ensure that the extracted differences are due to anatomical changes rather than equipment variance, it becomes essential to monitor and to assess the MRI system stability. In the first chapter of the dissertation, a method for monitoring pre-clinical MRI system performance is discussed. The technique developed during the study provides a fast and simple method to monitor pre-clinical MRI systems but also has applications for all areas of MRI. The second chapter describes the development of a 3D UTE MRI method for pulmonary imaging in freely breathing mice. The development of the 3D UTE sequence for pulmonary MRI has demonstrated its ability to collect images without noticeable motion artifacts and with appreciable signal from the lung parenchyma. Furthermore, images at two distinct respiratory phases were reconstructed from a single data set, providing functional information of the rodents' lungs. Finally, in the third chapter, 3D ¹⁹F UTE MRI is evaluated for imaging in vivo distributions of perfluorocarbon (PFC) nanoemulsions for measuring pulmonary inflammation. Building upon the development of pulmonary imaging, fluorinated contrast agents made from PFCs were used to target immune cells in response to pulmonary pathology. Both 3D ¹H and ¹⁹F UTE MRI were used to acquire pulmonary images of mouse models documented to have pulmonary pathology. Even though the mice had confirmed elevation in alveolar macrophage counts, no visible ¹⁹F signal accumulation within the pulmonary tissue was observed with MRI.