The ubiquitin system is involved in almost all aspects of protein function and cell fate and is thought to play an important role during neural development. Defects within the ubiquitin system have been linked to a range of neuro-degenerative diseases including Parkinson’s and Alzheimer’s disease. De-ubiquitylating enzymes function downstream in the ubiquitin pathway having potential to act as the final arbiters of substrate fate and function. Several studies have shown that de-ubiquitylating enzymes play important roles in the growth, function and maintenance of neurons. The substrate-specific de-ubiquitylating enzyme USP9X is highly expressed in the developing central nervous system. In vitro analyses have shown that USP9X is highly expressed in neural stem cells while expression remains at lower levels in more differentiated neural cell types. As the human and mouse USP9X genes share a 97% nucleotide identity within the coding sequence, this study uses the mouse as a model to analyse the role of USP9X during mammalian neural development. Previous studies have shown that loss of USP9X in the pre-implantation mouse embryo results in pre-implantation lethality. To circumvent this early developmental stage and analyse USP9X function in the developing brain we utilized a conditional knockout strategy involving the Cre/loxP recombination system. Using the Cre/loxP recombination system we permanently disable USP9X via exon removal specifically in the CNS during embryonic development. Two models were utilised, the first disabling USP9X in the whole CNS using Nestin-Cre mediated deletion and the second disabling USP9X in the dorsal telencephalon (dorsal forebrain) using Emx1-Cre. Using these models, USP9X is targeted in neural stem cells / neural progenitor cells prior to differentiation. This approach presents the ability to examine the effects of loss of USP9X on neural progenitor cells as well as neuronal and glial cells that derive from these progenitors.