Development of physiologically relevant cellular models, with strong translatability to human pathophysiology, is critical for identification and validation of novel therapeutic targets. Cell types derived from induced pluripotent stem cells (iPSCs) provide an important resource for modelling native biology in human cells and tissues for drug discovery. Understanding the phenotypic and functional relevance of these iPSC derived cells and tissues and how well they represent human biology is vital and as such we have developed tool iPSC-lines and techniques to optimize and monitor differentiation. Applying CRISPR/Cas9, Next Generation Sequencing (NGS), functional testing and advanced imaging techniques to iPSC model validation, we have established a platform that enables an accurate assessment of their benefits, maturity, gaps and challenges, as well as application in a drug discovery setting. Data presented will be from a key kidney model system we have developed to examplify our platforms. This will describe the validation and application of our kidney model, using SIX2 and NPHS1 markers non-invasively in real-time, to trace early nephron commitment and podocyte-maturation in the same cell. In adition, we will also describe how we use transcriptomic analysis by NGS, in addition to functional assays, to get the most from our iPS derived 3D cell models.