Understanding cell functioning at the nanoscale has been hampered in part by the diffraction limited resolution of optical microscopy. We developed partial wave spectroscopic (PWS) microscopy that is capable of quantifying statistical properties of cell structure at the nanoscale. Our animal and human studies demonstrated that alterations in the nanoscale cell architecture is one of the earliest events in carcinogenesis and precedes any other known morphological changes at larger length scales (i.e. microarchitecture).