The Cyclin-dependent kinase-like 5 (CDKL5) gene encodes for a serine-threonine kinase sharing homology to Mitogen-activated kinases (MAPKs) and Cyclin-dependent kinases (CDKs). Recently, mutations in the CDKL5 gene have been identified in the patients with neurodevelopmental disorders associated with epilepsies, such as West syndrome or atypical Rett syndrome, suggesting its critical role in neurodevelopment. However, neither its molecular functions or pathomechanisms caused by its mutations are largely unknown. Aiming to elucidate these problems, we have taken multidimensional strategies, combining an unbiased interactome approach and a targeted loss-of-function (LOF) approach. For the interactome approach, we performed the yeast two-hybrid screening and identified several CDKL5 interacting proteins. For the LOF approach, we have generated the Cdkl5 knockout mouse and analyzed the neurological phenotypes. The combination of these approaches suggested us possible mechanisms of CDKL5 regulating neural functions during development.