Aim To compare the effect of several materials on the attachment of periodontal ligament (PDL) fibroblasts to experimentally perforated root surfaces. Methodology Root specimens (size 5 x 5 mm) were obtained from extracted human molar teeth and perforations with a 1 mm diameter were created. One group was kept as a control and the rest were repaired with the following materials: Amalgam, Dyract, IRM, Super Bond C&B and Mineral trioxide aggregate (MTA). PDL fibroblasts were placed at a density of 8 x 104 cells on the root specimens, incubated on tissue culture inserts (48 h) and then transferred to 48 well-plates. MTT assays were performed at 48 and 96 h for PDL fibroblast survival. Cell attachment was observed using confocal microscopy on days 2 and 5. Total RNAs from the root specimens were isolated on day 5 and type I collagen (COL I) and Runt-related transcription factor 2 (Runx2) mRNA expressions were checked using Quantitative-Polymerase Chain Reaction (QPCR). For the MTT assay and QPCR, one-way analysis of variance (anova) and Tukey HSD multiple comparison tests were used to compare the groups. Results Mineral trioxide aggregate resulted in a significantly higher cell density (P < 0.001). Dyract, IRM and Super Bond C&B groups had a lower cell density when compared with the control and MTA groups at 48 h (P < 0.001). Confocal microscopy revealed that, among the experimental groups, the MTA group had the largest viable cell population over the restoration site when compared with the other materials; however, reduced cell attachment was noted in all groups when compared with the control. Increased Runx2 mRNA expressions were noted in MTA (P < 0.001) and IRM (P < 0.01) groups when compared with control and other tested materials. COL I transcripts were increased in IRM (P < 0.01), D, C&B and MTA (P < 0.001) when compared with the control. Conclusion Mineral trioxide aggregate provided a more favorable environment for PDL cell adhesion and growth.