ABSTRACT Electronic cigarettes (e-cigs) have been rapidly increasing in use and are touted as less harmful than cigarettes for smokers, while at the same time promoting concerns for adolescents and young adults who initiate e-cig use. The Food and Drug Administration (FDA) has deemed regulatory authority over e-cig product design and marketing. To do this, the FDA needs scientific data to support evidence-based policy decisions. The FDA views e-cigs as having the potential to reduce harm for current smokers without many of dangerous toxicants found in cigarette smoke that cause cancer, cardiovascular, and respiratory disease. However, this remains unproven, and there has been little scientific study of human target organ toxicity (e.g., the respiratory tract). Central to considering a potential harm reduction or unique effects of e-cigs, biomarker studies of exposure and harm to e-cig aerosols are needed. E-cigs may induce inflammation, which is a hallmark of lung disease. An important component of this involves oxidative stress, resulting in DNA damage. Most genetic studies of cigarette smoking and e-cig vapors to date focus on nuclear DNA. However, given that mitochondrial DNA (mtDNA) is vulnerable to oxidative stress and has an increased accumulation rate of mutations relative to nuclear DNA, mtDNA may be a novel target of toxic effects. This study will focus on the effects of e-cig use of smokers on mtDNA in the lung and nasal tract. Nasal epithelia gene expression has been related to cancer development in the lung, suggesting that the use of nasal samples provides for a non-invasive test. Here, we propose to leverage a NIDA-funded, IRB approved study, to evaluate the lungs of smokers by bronchoscopy who are switched to e-cigs, namely the NIDA Standardized Research E-cig (SREC). Smokers, following baseline bronchial and nasal brushings, are randomized to controls (continued smoking their usual brand), complete switching to the SREC or nicotine replacement therapy (NRT). A follow-up bronchial and nasal brushing will be done after 2 months of use. The overall hypothesize of this study is that mtDNA alterations, as biological indicators of harm, will be reduced in smokers who switch to e-cigs, but the effect will be less compared to quitting with NRT, and will support the use of mtDNA as biomarkers of effect for future e-cig evaluation. The Specific Aims for this project is: 1) to assess changes of mtDNA genetic features (mutations and copy numbers) over 2 months in the bronchial and nasal epithelium of smokers randomized to continued smoking, exclusive e-cig, or NRT use; 2) to investigate if changes in mtDNA alterations are associated with lung inflammation and gene expression; 3) to compare mtDNA alterations of smokers between bronchial and nasal samples. The significance of this study is to document the extent to which mtDNA alterations as a biomarker of harm are reduced following the use of e-cigs and provide evidence for the use of nasal epithelium for noninvasive biomarkers of harm. This study is also important, as it will allow us to discover novel reversible mtDNA alterations as biomarkers of toxic effects for smokers switching to e-cigs.