High-density lipoprotein (HDL) cholesterol levels are inversely correlated with the development of cardiovascular disease. To date, genetic association studies have explained only a small proportion of the overall variance in HDL cholesterol. Further studies are needed, within practice-based cohorts, to place genetic findings into context alongside important clinical variables (eg, age, sex, body mass index, medication use, and clinical comorbidity). The Marshfield Clinic Personalized Medicine Research Project database was designed for large-scale studies of genetic epidemiology in a clinical practice-based setting. Because of its size and its unique practice-based design, this resource will provide adequate statistical power for the assessment of genetic findings related to HDL cholesterol level within the context of covariates known to modify lipid homeostasis. The authors report construction and validation of novel electronic phenotyping algorithms that can be used to model individual baseline HDL cholesterol levels within this practice-based resource. Because these algorithms were developed in a setting that reflects routine clinical care, future genetic studies using these algorithms within practice-based DNA biobanks should facilitate the identification of markers with optimal effect size after adjustment for known clinical factors contributing to the overall variance in HDL cholesterol level within the community.