It is becoming increasingly clear that stem cell function and differentiation state are affected by the physical environment of the stem cell, and the stem cells physical properties or physical phenotypes. Physical phenotypes include how the cell responds to forces in its environment and its subcellular structure. This presentation will be primarily focused on subcellular structure, or structural phenotype. I will present two different techniques to quantitatively assess structural phenotype. The first is digital holographic microscopy (DHM), which is a marker-free method for assessing protein density within cells. The second is confocal microscopy, in which I used an anti-HP1α label for heterochromatin to deduce the distribution of chromatin and how it changes during cell differentiation. With both of these techniques, I observed significant changes in the structural phenotype of HL60 cells as they differentiated into three different lineages. I extended these techniques to pluripotent stem cells (PSCs), and assessed how the subcellular structure changed as PSCs make their first fate decisions. I will discuss the changes observed in the distribution of chromatin, novel ways to quantify it, and how it can be used as a biomarker for stem cell function and differentiation state. Furthermore, I will discuss how physics-based concepts and techniques can lead to a minimally invasive, quantitative toolbox for assessing stem cells, both in the laboratory and in the clinic.