The health and viability of cells and tissues in the human body depend on the functional integrity of proteins. A small number of long-lived proteins, including the crystallins in the lens of the eye, evade protein turnover, a typical cellular mechanism for repair and regeneration, and remain extant throughout life. The cumulative effect of post-translational modifications on the structure, function, and conformation of these long-lived proteins records the history of molecular aging in an individual. Along with absence of protein turnover, the optical accessibility, transparency, and age-related spatial order make the lens an ideal target for in vivo assessment of molecular aging. Accordingly, this doctoral thesis investigated the hypothesis that age-related perturbations that alter the protein environment in the human lens can be detected and monitored as a quantitative biomarker of molecular aging detectable by quasi-elastic light scattering (QLS). To test this hypothesis, QLS was applied in vitro and in vivo to study time-dependent changes in lens proteins. Water-soluble human lens protein extract was used in vitro as a model system that mimics the lens fiber cell cytoplasm. The effects of long-term incubation (nearly one year, proxy for aging), oxidative stress, ionizing radiation, metal-protein and pathogenic protein-protein interactions were investigated by QLS as a function of time. In vitro results were validated by protein gel electrophoresis and transmission electron microscopy. In vivo, age-dependent changes in lens proteins were assessed in healthy subjects across a broad age-range (5–61 years of age). Pathogenic protein aggregation in the lens was examined in vivo using Down syndrome (DS) subjects, a common chromosomal disease associated with an age-related Alzheimer’s disease (AD)-linked lens phenotype. Results obtained from the in vitro studies noted, for the first time, QLS detection of long-term supramolecular changes in a complex lens protein model system. Our FDA-approved QLS device was successful in assessing age-dependent lens protein changes in a clinical study at Boston Children’s Hospital (BCH). In two landmark studies conducted at BCH, we detected statistically significant AD-related lens protein changes in DS subjects aged 10–20 years, when compared with age-matched controls. These studies are the first clinical application of QLS in DS, and demonstrate protein changes in DS earlier than any previously reported studies. Due to the discrepancy in chronological and biological age and the lack of an objective index for the latter, we propose the application of QLS in the human lens as a quantitative biomarker of molecular aging.