The differences of the cytogenotoxicity and proteins expression of human B-cell lymphoblastoid cells exposed to cigarette smoke condensates (CSCs) from two kinds of cigarettes were detected with CCK-8 assay, comet assay, protein microarray and western blot assay in vitro. Human B-cell lymphoblastoid cell line was exposed to CSCs from two cigarettes (which delivers approximately 3mg tar, 0.3mg nicotine, 3mg CO per cigarette for cigarette 1 and 15mg tar, 1.3mg nicotine, 15mg CO per cigarette for cigarette 2), and the exposure doses were 2.5, 5.0, 7.5, 10.0 and 12.5×10−3 cigarettes/ml of CSCs for 24h in CCK-8 assay, 6.0, 8.0, 10.0, 12.0 and 14.0×10−3 cigarettes/ml of CSCs for 4h in comet assay, and 10.0×10−3 cigarettes/ml of CSCs for 4h in protein levels analysis. The results of CCK-8 assay and comet assay in the present study suggested that the cytogenotoxicity in cigarette 2 group was significantly higher than that in cigarette 1 group. The results of protein microarray and western blot assay showed that there were the differences of the expression levels of four proteins (i.e., RAR-β, 14-3-3 sigma, XPF, and p57Kip2 Ab-7) between cigarette 1 group and cigarette 2 group. Hence, it is possible that the RAR-β, 14-3-3 sigma, XPF, and p57Kip2 Ab-7 proteins serve as the molecular biomarkers in studying the cytogenotoxicity induced by CSCs.