When developing new drugs, it is critical to understand the permeability, absorption, and transport mechanisms of new therapeutics in relevant biological systems. The OrganoPlate® is a microfluidic platform for 3D cell culture of multiple tissue types in a standard 384 well plate format that is compatible with automation workflows. Here, we compare permeability assays in Caco‑2 intestinal tubule models cultured in the OrganoPlate to those cultured in a conventional permeable filter support (Transwell®) system.