Graphical Abstract Highlights d d-pcdh adhesive interactions are preferentially homophilic with distinct affinities d d1-and d2-pcdhs form canonical adhesive dimers with divergent specificity regions d Ectodomain-mediated cis interactions are not observed, in contrast to clustered pcdhs SUMMARYNon-clustered d1-and d2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the molecular interactions underlying these functions, we used solution biophysics to characterize binding of d1-and d2-protocadherins, determined crystal structures of ectodomain complexes from each family, and assessed ectodomain assembly in reconstituted intermembrane junctions by cryoelectron tomography (cryo-ET). Homophilic trans (cell-cell) interactions were preferred for all d-protocadherins, with additional weaker heterophilic interactions observed exclusively within each subfamily. As expected, d1-and d2-protocadherin trans dimers formed through antiparallel EC1-EC4 interfaces, like clustered protocadherins. However, no ectodomain-mediated cis (same-cell) interactions were detectable in solution; consistent with this, cryo-ET of reconstituted junctions revealed dense assemblies lacking the characteristic order observed for clustered protocadherins.Our results define non-clustered protocadherin binding properties and their structural basis, providing a foundation for interpreting their functional roles in neural patterning.