CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales. ; This work was financially supported by the following grants: CSD2007-00050 from the Spanish Ministry of Science (http://www.mineco.gob.es/portal/site/mineco/idi), grant SGR-1430 from the Catalan Government (http://web.gencat.cat/ca/temes/tecnologia/), grant ERC-2011-AdG-294653-RNA-MAPS from the European Community financial support under the FP7 (https://erc.europa.eu/) and grant R01MH101814 by the National Human Genome Research Institute of the National Institutes of Health (https://www.genome.gov/), to RG. Ramón y Cajal RYC-2011-08851 and Plan Nacional BIO2011-27220, both from the Spanish Ministry of Science (http://www.mineco.gob.es/portal/site/mineco/idi), to RJ. We also acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 (http://www.mineco.gob.es/portal/site/mineco/idi). We also acknowledge the support of the CERCA Programme / Generalitat de Catalunya (http://web.gencat.cat/ca/temes/tecnologia/). This research was partly supported by the NCCR RNA & Disease funded by the Swiss National Science Foundation (http://www.nccr-rna-and-disease.ch/).