Kidney organoids (KOs) are being actively developed and used as models for evaluating nephrotoxicity, which is an important process during drug development. To evaluate human pluripotent stem cell-derived KOs, various lineage markers have been used to confirm KO differentiation via quantitative real-time-PCR and western blotting. However, as these are qualitative evaluations, there are currently limitations in evaluating how similar differentiated KOs are to actual human kidneys. Thus, in this study, we utilized RNA-sequencing (21 organs; n = 7361) derived from the GTEx database to create a transcriptome-based kidney-specific gene expression panel (KiGEP) and developed a quantitative calculation algorithm (the KiGEP algorithm) to assess the similarity between human pluripotent stem cell-derived KOs and human kidneys. Thus, the KiGEP algorithm allows quantitative quality assessments of KOs, providing important information for the development of high-quality KOs for drug development and regenerative medicine applications.