In the present study, the cyto-genotoxic effects of 12 CSCs prepared from a diverse set of cigarettes on human B lymphoblastoid cells were compared using five in vitro assays. The cells were exposed to CSCs at doses of 2.5, 5.0, 7.5, 10.0, and 12.5×10−3 cigarette/ml for 24h in neutral red uptake and CCK-8 assays, at doses of 1.0, 2.0, 3.0, 4.0, and 5.0×10−3 cigarette/ml for 3h in cell apoptosis assay, at doses of 6.0, 8.0, 10.0, 12.0, and 14.0×10−3 cigarette/ml for 4h in comet assay, and at doses of 1.0, 2.0, 4.0, 6.0, and 8.0×10−3 cigarette/ml for 4h in micronucleus assay. The potency of 12 CSCs to induce corresponding toxic effects in each assay was calculated, and the correlations between the results in five assays were analyzed. Our investigation showed that the results of 12 CSCs in CCK-8 and cell apoptosis assays were positive, the results of 11 CSCs in neutral red uptake and comet assays were positive, and 9 CSCs could induce significantly the micronuclei in micronucleus assay. It was found that the potency to induce the cytotoxic effects among 12 CSCs ranged 9.694 folds in neutral red uptake assay and 6.43 folds in CCK-8 assay, the potency to induce cell apoptosis among 12 CSCs ranged 8.191 folds, the potency to induce DNA damage among 12 CSCs ranged 29.199 folds, the potency to induce micronuclei among 12 CSCs ranged 5.879 folds. Moreover, the good correlations were found between any two assays. It was suggested that the cyto-genotoxicity of CSCs from different brands of cigarettes varied greatly, comet assay might be a sensitive assay in assessing the genotoxicity induced by CSCs.