In mammals, neurons are highly differentiated and play distinctive functions even in the same brain region. We found a novel cadherin-related neuronal receptor (Cnr) gene family by studying Fyn-binding activity in mouse brain. CNR1 protein is located in the synaptic junction and forms a complex with Fyn. Sequence analysis of eight Cnr products of approximately 20 genes indicates that these comprise a novel cadherin family of the cadherin superfamily. The expression patterns of each member of this novel family were grossly similar to each other but restricted to subpopulations of neurons of the same type. The diversity of the Cnr family genes suggests that there are molecular mechanisms that govern highly differentiated neural networks in the mammalian CNS.