Human pluripotent stem cells (hPSCs) are known to harbor chromosomal aberrations, affecting their tumorigenic potential. We established a strategy to identify cancer-related point mutations in hPSCs, detecting recurrent mutations in over 20 genes, alongside those previously detected in p53. Importantly, naive hPSCs harbor, on average, four times more mutations than their primed counterparts, which appear primarily in pathways inhibited during naive conversion. Such cancer-related mutations should be taken into consideration in future applications, especially in clinical contexts. Copyright © 2019 Elsevier Inc. All rights reserved.