In the present study, the cytotoxic effects of five prosthodontic materials on the L929 cell line were assessed by flow cytometry (FCM), reverse transcription PCR (RT-PCR), and MTT (3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazoli-umbromide) assay. The cells were treated with eluates resin (RE), pressable ceramics (PC), Co-Cr alloy-porcelain (CC), Ni-Cr alloy-porcelain (NC), and diatomite ceramics (DC). The cytotoxicity of all the materials tested by the MTT assay was grade 1. By FCM analysis, apoptosis rates of DC and PC were low, with no significant difference from the control (p > 0.05). The rest of the groups induced much higher apoptosis rates (p < 0.05), with the highest in the RE group. The necrotic cell levels of RE was also significantly increased (p < 0.05). Bcl-2 and Bax mRNA expression were determined by RT-PCR, and the Bax/Bcl-2 ratio in the DC and PC groups were not significantly different from the control (p > 0.05), whereas CC, NC, and RE groups showed significant differences (p < 0.05). Taken together, the results suggest that FCM and RT-PCR analyses can supplement the traditional MTT assay in evaluating the cytotoxicity of prosthodontic materials for selecting highly biocompatible materials.