Tissue barrier function is directly mediated by tight junction transmembrane proteins known as claudins. Cells that form tight junctions typically express multiple claudin isoforms, which suggests that heterotypic (head-to-head) binding between different claudin isoforms may play a role in regulating paracellular permeability. To test whether claudins are heterotypically compatible, we developed an assay system using HeLa cells, a claudin-null cell line which expresses other tight junction proteins, including occludin, junction adhesion molecule A, and zonula occludens-1, -2, and -3. HeLa cells stably transfected to express different claudins are cocultured, then subsequently analyzed for the ability to coimmunopurify. Using this approach, we have found that claudin-1, claudin-3, and claudin-5 are heterotypically compatible. In contrast, two closely related claudins, claudin-3 and claudin-4, are incompatible. Differential claudin-binding specificity is likely to have downstream effects on the regulation of tight junction composition and permeability.