Planar cell polarity (PCP) in epithelial cells is essential for the organization of tissues and their functions. The conserved non-canonical Wnt/PCP pathway regulates this process in both Drosophila and vertebrates. However, recent studies have revealed that a similar set of genes, which may not be related to PCP, regulates oriented cell movement during development. In the present review, recent findings on neural migration in zebrafish hindbrain and axonal guidance in mouse forebrain and spinal cord are discussed. Future analyses on defects in vertebrate PCP mutants will provide novel insights into the conserved and diverse roles of non-canonical Wnt/PCP pathway genes in vertebrate brain development.