In species as varied as humans and flies, humoral/central nervous system barrier structures are a major obstacle to the passive penetration of small molecules including endogenous compounds, environmental toxins, and drugs. In vivo measurement of blood-brain physiologic function in vertebrate animal models is difficult and current ex vivo models for more rapid experimentation using, for example, cultured brain endothelial cells, only partially reconstitute the anatomy and physiology of a fully intact blood-brain barrier (BBB). To address these problems, we and others continue to develop in vivo assays for studying the complex physiologic function of central nervous system (CNS) barriers using the fruit fly Drosophila melanogaster (Dm). These methods involve the introduction of small molecule reporters of BBB physiology into the fly humoral compartment by direct injection. Since these reporters must cross the Dm BBB in order to be visible in the eye, we can directly assess genetic or chemical modulators of BBB function by monitoring retinal fluorescence. This assay has the advantage of utilizing a physiologically intact BBB in a model organism that is economical and highly amenable to genetic manipulation. In combination with other approaches outlined here, such as brain dissection and behavioral assessment, one can produce a fuller picture of BBB biology and physiology. In this chapter, we provide detailed methods for examining BBB biology in the fly, including a Dm visual assay to screen for novel modulators of the BBB.