The authors adapted the bacterial CRISPR RNA/Cas9 system to engineer the Drosophila genome, demonstrating that Cas9-mediated genomic modifications are efficiently transmitted through the germline. The RNA-guided Cas9 system can be rapidly programmed to generate targeted alleles for probing gene function in Drosophila. The study shows that a single chiRNA can guide Cas9 to a specific genomic sequence to induce double-strand breaks (DSBs) that are imperfectly repaired by nonhomologous end joining (NHEJ), while multiplex targeting can be used to generate large defined deletions. The authors also successfully replaced the yellow gene with an attP docking site using a single ssODN donor template. Germline transmission rates for these modifications ranged from 1.1% for multiplex-mediated deletions to 5.9% for single chiRNA-induced NHEJ. The lack of detectable off-target effects suggests high specificity of targeting by the CRISPR RNA/Cas9 system. Overall, the results demonstrate the efficient generation of genome modifications via the CRISPR RNA/Cas9 system in Drosophila and for the first time show germline transmission of Cas9-mediated modifications.The authors adapted the bacterial CRISPR RNA/Cas9 system to engineer the Drosophila genome, demonstrating that Cas9-mediated genomic modifications are efficiently transmitted through the germline. The RNA-guided Cas9 system can be rapidly programmed to generate targeted alleles for probing gene function in Drosophila. The study shows that a single chiRNA can guide Cas9 to a specific genomic sequence to induce double-strand breaks (DSBs) that are imperfectly repaired by nonhomologous end joining (NHEJ), while multiplex targeting can be used to generate large defined deletions. The authors also successfully replaced the yellow gene with an attP docking site using a single ssODN donor template. Germline transmission rates for these modifications ranged from 1.1% for multiplex-mediated deletions to 5.9% for single chiRNA-induced NHEJ. The lack of detectable off-target effects suggests high specificity of targeting by the CRISPR RNA/Cas9 system. Overall, the results demonstrate the efficient generation of genome modifications via the CRISPR RNA/Cas9 system in Drosophila and for the first time show germline transmission of Cas9-mediated modifications.