Transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are new classes of genome-editing tools that target desired genomic sites in mammalian cells (Miller et al., 2011; Hockemeyer et al., 2011; Cong et al., 2013; Mali et al., 2013; Jinek et al., 2013). TALENs bind as a pair around a genomic site in which a double-strand break (DSB) is introduced by a dimer of FokI nuclease domains. Recently published type II CRISPR/Cas systems use Cas9 nuclease that is targeted to a genomic site by complexing with a synthetic guide RNA that hybridizes a 20-nucleotide DNA sequence (‘‘protospacer’’) beginning with G and immediately preceding an NGG motif recognized by Cas9—constituting a G (N) 19NGG target DNA sequence—resulting in a DSB three nucleotides upstream of the NGG motif (Jinek et al., 2012). However it is generated, the DSB instigates either nonhomologous end-joining(NHEJ), which is error-prone and conducive to frameshift mutations (indels) that knock out gene alleles, or homology-directed repair (HDR), which can be exploited with the use of an exogenously introduced double-strand or single-strand DNA repair template to knock in or correct a mutation in the genome. We recently reported the use of a TALEN genome-editing system to rapidly and efficiently generate mutant alleles of 15 different genes in human pluripotent stem cells (hPSCs) as a means of performing rigorous disease modeling (Ding et al., 2013); the proportions of clones bearing at least one mutant alelle ranged from 2%–34%. Although one example of the use of CRISPRs in hPSCs has been reported (Mali et al., 2013), the efficiency of allele targeting was only 2%–4%, but this study, unlike our approach, did not involve a cell-sorting step. We sought to compare the relative efficacies of CRISPRs and TALENs targeting the same genomic sites in the same hPSC lines with the use of the same delivery platform as we described previously (Ding et al., 2013). In the TALEN genome-editing system, we used the CAG promoter to cotranslate (via a viral 2A peptide) each TALEN with green fluorescent protein (GFP) or red fluorescent protein (RFP). For CRISPRs, we subcloned a human-codon-optimized Cas9 gene with a C-terminal nuclear localization signal (Mali et al., 2013) into the same CAG expression plasmid with GFP, and we separately expressed the guide RNA (gRNA) from a plasmid with the human U6 polymerase III promoter (Mali et al., 2013). The 20 nucleotide protospacer sequence for each gRNA was introduced using polymerase chain reaction (PCR)-based methods. Whether using TALENs or CRISPRs, equal amounts of the two plasmids were coelectroporated into hPSCs—either 25 μg of each plasmid or 15 μg of each plasmid along with 30 μg of a DNA repair template if attempting knockin—and subjected to fluorescence-activated cell sorting (FACS) after 24–48 hr, clonal expansion of single cells, and screening for mutations at the genomic target site via PCR. We designed gRNAs matching G (N) 19NGG sequences in seven loci in six genes—AKT2, CELSR2, CIITA, GLUT4, LINC00116, and SORT1—that we had previously successfully targeted with TALENs (Ding et al., 2013) and in one locus, in LDLR, that we had not. We found that in our system CRISPRs consistently and substantially outperformed TALENs across loci and hPSC lines (see Table S1 available online). The TALENs yielded clones with at least one mutant allele at efficiencies of 0%–34%, but matched CRISPRs yielded mutant clones at efficiencies of 51%–79%(Table S1). Just as with …