Analyzing transport of biliary metabolites is essential to predict pharmacokinetics and hepatotoxicity during drug development. A functional impairment of hepatobilary transporters, such as bile salt export pump (BSEP) and multidrug resistance-associated protein 2 (MRP-2), is strongly associated with an increased risk of cholestatic liver injury. Here, we describe a 3D high-content screening assay to study hepatobiliary transporter function in InSphero human liver microtissues. Confocal imaging and automated image analysis were used to quantify BSEP and MRP-2-mediated efflux of fluorescent substrates into bile canaliculi.