The tightly regulated permeability of the blood-brain barrier (BBB) greatly limits the range of therapeutic treatment options for diseases of the central nervous system (CNS). The use of focused ultrasound (FUS), in conjunction with circulating microbubbles (MBs), is a unique approach whereby the transcranial application of acoustic energy, focused within targeted brain areas, can be used to induce a noninvasive, transient, and spatially precise increase in BBB permeability. This can provide an avenue for the delivery of therapeutic agents from systemic circulation into the brain. While this approach continues to show great promise in animal models and has entered clinical testing, there remains a need for preclinical research to investigate the long-term effects of repeated FUS + MB exposure on cerebrovascular health and neurological function, as well the efficacy and pharmacokinetics of specific drugs following delivery. Additionally, there is a need for monitoring strategies that can more precisely predict bioeffects resulting from treatments. Here we will describe two approaches to study FUS + MB-mediated BBB permeability enhancement in rodent models: MRI-guided FUS + MB exposure and in vivo two-photon fluorescence microscopy experiments. The aims of this chapter are to outline each procedure, present options for experimental design, and highlight important considerations for the collection and interpretation of data.