Biomarkers of potential harm (BoPH) are indicators of biological perturbations in response to smoking, which may contribute to smoking-related disease. In this review, a project of the CORESTA Biomarkers Sub-Group, we critically assessed the available lung biomarkers of biological effect / BoPH in human lung disease for potential use in evaluation of the effects of tobacco and nicotine products. A Scopus literature search was conducted on lung disease biomarkers that had been used in a clinical setting in humans over the last ten years. Inclusion criteria included human studies only, data on the association of cigarette smoking, smoking cessation with the biomarker and data on smoking vs. non-smoking, preferably with data on changes with smoking cessation. This process identified 1171 papers which were then further screened using commercially available software (Sciome Active Screener). We identified 68 publications that met our preset criteria. This identified five potential sources of biomarkers: Imaging (~9 papers), Blood (~36 papers), Lung Sampling, (~14 papers), Lung Function (~14 papers), and Miscellaneous (~1 paper). This critical review identified several physiological and biochemical measures that are potentially relevant for evaluating the impact of tobacco products on lung health.