Molecular epidemiology is a powerful tool, integrating laboratory methods into epidemiology, to better understand the biological underpinnings of health and disease in populations. Recent advances in assay methods, data processing, and analytic tools have allowed for the application of omics profiling in large-scale population-based studies. The metabolome, long considered the end product of other ‘-omes’, reflects both endogenous and exogenous inputs. Incorporating metabolomic profiling into molecular epidemiology studies has enhanced our understanding of metabolic perturbation in disease development and allowed for explorations of biologic influences of modifiable environmental factors, such as aspects of diet and lifestyle. We have leveraged the Nurses’ Health Studies, ongoing prospective cohort studies with decades of follow-up, to investigate the role of the metabolome in the development of cancer and cardiometabolic diseases. This talk will cover critical aspects of study design in molecular epidemiology, considerations for analysis of metabolomic profiles, and associations of metabolomics with lifestyle factors and risk of chronic diseases.