Potential reduced exposure products (PREPs) to tobacco toxicants may have promise in reducing tobacco-related morbidity or mortality or may promote greater harm to individuals or the population. Critical to determining the risks or benefits from these products are valid human clinical trial PREP assessment methods. Such an assessment involves determining the effects of these products on biomarkers of exposure and effect, which serve as proxies for harm, and assessing the potential for consumer uptake and abuse of the product. This article identifies critical methodologic issues associated with PREP assessments, reviews the methods that have been used to assess PREPs, and describes the strengths and limitations of these methods. Additionally, recommendations are provided for clinical trial PREP assessment methods and future research directions in this area based on this review and on the deliberations from a National Cancer Institute sponsored Clinical Trials PREP Methods Workshop.