CRISPR-based genetic screening directly in mammalian tissuesin vivois challenging due to the need for scalable, cell-type selective delivery and recovery of guide RNA libraries. We developed anin vivoadeno-associated virus-based and Cre recombinase-dependent workflow for cell type-selective CRISPR interference screening in mouse tissues. We demonstrate the power of this approach by identifying neuron-essential genes in the mouse brain using a library targeting over 2000 genes.