Here we present the solution characterization of mouse LPHN3-OLF, FLRT3-LRR, the crystal structure of LPHN3-OLF alone in two different conformations, its complex with the LRR domain of FLRT3 and a characterization of the association including the effect of the Ser247Ala human mutation. Our structural analysis suggests that the high affinity interaction between LPHN3-OLF and FLRT3 is necessary for some aspect of the development of glutamatergic synapses.