The Cas9 endonuclease from the microbial adaptive immune system CRISPR can be easily programmed to bind or cleave specific DNA sequence using a short RNA guide. Cas9 is enabling the generation of more realistic disease models and is broadening the number of genetically-tractable organisms that can be used to study a variety of biological processes. The Cas9 nuclease can also be modified to modulate transcription, alter epigenetic states, and track the dynamics of chromatin in living cells. In this presentation we will look at the latest developments and applications of the Cas9 nuclease for understanding the function of the mammalian genome. We will also look at the on-going challenges as well as future prospects of the technology.