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Background Cigarette smoking remains one of the leading public health threats worldwide. Electronic cigarettes (e-cigs) provide an alternative to conventional cigarette smoking; however, the evidence base of risks and benefits of e-cig use is new and growing. In this cross-sectional pilot study, the effect of e-cig use on biological profiles in saliva and gingival crevicular fluid (GCF) was assessed and compared with the profiles of cigarette smokers (CS), dual users, and non-users. The systemic inflammatory mediators between e-cig users (EC) and these other groups were also assessed. Methods This pilot cross-sectional study recruited volunteer participants consisting of four groups, non-smokers (NS), CS, EC, and dual EC and cigarette smokers (DS). Saliva and GCF samples were collected and analyzed for biomarkers of inflammation, oxidative stress, anti-inflammatory lipid mediators, tissue injury and repair, and growth factors with immunoassay (enzyme-linked immunosorbent assay and Luminex). Results Smoking status was confirmed via salivary cotinine. Prostaglandin E2 level was significantly increased in CS compared with EC and DS, but not significantly different in EC and DS groups compared with non-smokers (NS). Statistically significant differences were observed between groups of EC and NS (myeloperoxidase [MPO], matrix metalloproteinase-9) as well as between DS and EC for biomarkers of inflammatory mediators (receptor for advanced glycation end products [RAGE], MPO, uteroglobin/CC-10); between groups of DS and NS for extracellular newly identified RAGE binding protein and between CS and NS for MPO. No statistically significant differences in biomarkers of immunity (S100A8, S100A9, galectin-3), tissue injury and repair (Serpine1/PAI-1) and growth factors (brain-derived neurotrophic factor, fibroblast growth factors, platelet-derived growth factor-AA, vascular endothelial growth factor, and others) were found between any of groups. Conclusion Statistically significant differences in measurable health outcomes were found between different smoking status groups, suggesting that smoking/vaping produces differential effects on oral health.