Biomonitoring has become a fundamental tool in both exposure science and clinical medicine. Despite significant analytical advances, the clinical use of environmental biomarkers remains in its infancy. Clinical use of environmental biomarkers poses some complex scientific and ethical challenges. The purpose of this paper is compare how the clinical and exposure sciences differ with respect to their interpretation and use of biological data. Additionally, the clinical use of environmental biomonitoring data is discussed. A case study is used to illustrate the complexities of conducting biomonitoring research on highly vulnerable populations in a clinical setting.