The diffusion of gases such as CO2 through lipid membranes is essential for cell function. Traditionally, gas transport across cell membranes was thought to be dominated by lipid-mediated diffusion. However, subsequent results suggest that proteins are capable of acting as gas pores, and that protein-mediated diffusion plays an important role. In order to investigate these systems in vitro, we have developed a method for measuring gas transport across giant unilamellar vesicles (GUVs) in a high-throughput microfluidic assay using fluorescence microscopy. Microfluidic systems enable rapid mixing that avoids the problem of unstirred layers. GUVs provide a robust platform for measuring properties of artificial membranes. This system is ideal for determining effects of lipid composition and incorporated membrane proteins.