The specialized cerebral microvascular endothelium interacts with the cellular milieu of the brain and extracellular matrix to form a neurovascular unit, one aspect of which is a regulated interface between the blood and central nervous system (CNS). The concept of this blood-brain barrier (BBB) as a dynamically regulated system rather than a static barrier has wide-ranging implications for pathophysiology of the CNS. While in vitro models of the BBB are useful for screening drugs targeted to the CNS and indispensable for studies of cerebral endothelial cell biology, the complex interactions of the neurovascular unit make animal-based models and methods essential tools for understanding the pathophysiology of the BBB. BBB dysfunction is a complication of neurodegenerative disease and brain injury. Studies on animal models have shown that diseases of the periphery, such as diabetes and inflammatory pain, have deleterious effects on the BBB which may contribute to neurological complications associated with these conditions. Furthermore, genetic and/or epigenetic abnormalities in constituents of the BBB may be significant contributing factors in disease etiology. Research that approaches the BBB as a dynamic system integrated with both the CNS and the periphery is therefore critical to understanding and treating diseases of the CNS. Herein, we review various methodological approaches used to study BBB function in the context of disease. These include measurement of transport between blood and brain, imaging-based technologies, and genomic/proteomic approaches.