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Background & Aim Genetic integrity of human pluripotent stem cells (hPSCs) is essential for the accuracy of the disease models and for the security of cell therapies that are use those cells. Because genetic abnormalities can accumulate during the generation of hPSC, their long term maintenance or during genome editing, it is mandatory to regularly check the genome of hPSCs. However, the current methods to assess genomic integrity of hPSC are not fully suitable for such regular screening. These approaches can be limited in term of resolution, flexibility, cost and time to process. Our aim is improving genetic screening of hPSC. Methods, Results & Conclusion Based on a large meta-analysis of all hPSC genetic abnormalities reported in more than 100 publications, we were able to exhaustively identify recurrent genetic abnormalities accumulating in hPSCs. We then developed a test (iCS-digital test) based on the droplet digital PCR technology that can detect more than 90% of these hPSC recurrent genetic abnormalities in DNA extracted from culture supernatant samples. This test was successfully used to detect copy number variations that arose during cell culture or gene editing. Hence, the iCS-digital test can be used to routinely screen genomic integrity in hPSCs, contribute to secure genome editing workflow, and reduce time and financial losses induced by the use of an abnormal hPSC lines.