In vivo loss-of-function studies are currently limited by the need for appropriate conditional knockout alleles. CRISPR/Cas9 is a powerful tool commonly used to induce loss-of-function mutations in vitro. However, the CRISPR components have been difficult to deploy in vivo. To address this problem, we developed CASAAV (CRISPR/Cas9-AAV-based somatic mutagenesis), a platform in which recombinant adeno-associated virus (AAV) is used to deliver tandem guide RNAs targeting a gene of interest and Cre, driven by a cell type selective promoter, to RosafsCas9GFP postnatal mice. Using this system, within one month it is possible to induce temporally controlled cell type-selective knockout of virtually any gene using only one mouse line. Here, we focus on knockout of genes in cardiomyocytes, although with minimal modifications the system could be adapted in inactivate genes in other AAV-transduced cell types.