Biomarkers can be useful tools in measuring the biological effects of tobacco product use. Although there is a small group of biomarkers that are typically used to assess the biological effect of tobacco use, there are few publications summarizing recent developments in this area. The purpose of this project was to investigate recent (past 5 years) publications to identify potential biomarkers that may be useful in assessment of the biological effect of tobacco product use. Candidate biomarkers were identified by investigating gene/protein associations in the published literature for three indications and a term: COPD, CVD, Lung Cancer (LC) and Tobacco Smoke (TS). Our approach used query terms, association words and database terms using the PolySearch web server and pattern recognition system-based relevancy ranking to identify gene-disease/term associations in the published literature. The search was limited to the ~50 highest ranked gene/proteins for each indication and term. The identified gene/proteins for each indication were then compared with the TS associated genes/proteins. This strategy identified 18 COPD + TS targets, 6 CVD + TS targets, and 10 LC + TS targets. Although no genes/proteins were found in all four conditions, 5 genes/proteins were common across COPD, CVD and TS, and 6 common genes/proteins across COPD, LC and TS. We identified enriched pathways using the Database for Annotation, Visualization, and Integrated Discovery (DAVID 6.8) represented by each set of biomarker candidates. Most enriched pathways were associated with immune and inflammatory response with the top-scoring enriched pathways for all three disease conditions were Jak- STAT signaling and cytokine-cytokine receptor interaction. This approach presents a promising tool for identification of emerging biomarkers to assess biological effects of tobacco product use.