The objective of this study was to evaluate the cytotoxicity of furcal perforation repair materials, GI and MTA, using cell culture technique.The extract of ProRoot MTA and Ketac Molar were treated on PDL cells in a 96-well tissue-culture plate. Cell proliferation after an incubation period of 3 days was determined by using MTT assay.The growth of cultured human periodontal fibroblast cells were suppressed by both perforation repair materials. The percent of cell viability in the Ketac Molar group was lower than in the ProRoot MTA group (P = .000).Although Ketac Molar has the advantage of adhering to dentine, it is more cytotoxic to the PDL cells than MTA. In selecting the perforation repair material, it is recommended not only to consider the sealing ability of the material with dentine but also the biocompatibility of material to the underlying tissue.