The partitioning-defective 3 (par3) gene encodes a protein with three postsynaptic density90/DiscslargeA/ZO-1 (PDZ) domains that is required for cell polarity establishment in metazoans. Par3 is a component of a protein complex that can include Cdc42-GTP, Par6 and atypical protein kinase Cs (aPKCs). We now describe the identification of a related human gene, Par3L. Both Par3L and Par3 are expressed as numerous alternatively spliced variants. Although Par3 expression appears to be ubiquitous, that of Par3L is more restricted. Multiple variants are often expressed simultaneously within a specific cell type or tissue. Although all of the Par3L/Par3 isoforms can associate with tight junctions in epithelial cells, they show different binding properties. No Par3L isoforms and only a subset of Par3 isoforms detectably bind aPKCs. These data suggest that aPKC binding or phosphorylation is not required for targeting of Par3/Par3L to cell-cell contacts. Par3L isoforms also show differential binding to Par6. Despite these differences, the N-terminal region of Par3L, like that of Par3, can disrupt the formation of tight junctions when ectopically expressed in Madin-Darby canine kidney (MDCK) cells.