The purpose of this study was to compare the cytotoxicity, induced apoptosis and/or necrosis, and apoptotic mechanisms in human periodontal ligament (PDL) fibroblasts treated with four different endodontic materials: White ProRoot mineral trioxide aggregate (MTA) (MTA/Dentsply; Tulsa Dental, Memphis, TN), Diaket (ESPE, Seefeld, Germany), Endion (VOCO, Cuxhaven, Germany), and CYMED 8410 (NANO, Kaohsiung, Taiwan). The effects of these four materials on the viability of PDL fibroblasts were determined by MTT (3-(4,5-dimethyl-thiazoyl)-2,5-diphenyl-SH-tetrazolium bromide) assay. Apoptotic pathways were evaluated via several mechanisms. Exposure to MTA for 24, 48, and 72 hours resulted in no significant differences in MTT reduction and viable cell number compared with controls. However, treatment of PDL fibroblasts with Diaket Endion, and CYMED 8410 for 24, 48, and 72 hours resulted in cytotoxicity with MTT and a reduction of viable cell number with trypan blue dye exclusion test compared with controls (from p < 0.05 to p < 0.001). Annexin V-FITC/PI staining showed that Diaket, Endion, and CYMED 8410 induced higher percentages of apoptosis and/or necrosis than in controls (45.6%, 25.5%, and 6.3%, respectively). Results of cell-cycle analyses were concordant with annexin V-FITC/PI staining findings. These results suggest that MTA is a very biocompatible filling material. However, Diaket, Endion, and CYMED 8410 are toxic to PDL fibroblasts in vitro. The main form of cell death induced by these filling materials was determined to be apoptosis and/or necrosis.