The main objective of a root end filling material is to provide an apical seal that prevents the movement of bacteria and the diffusion of bacterial products from the root canal system into periapical tissues. The aim of this study was to compare the microleakage of three root end filling materials Mineral trioxide aggregate (MTA), Glass ionomer cement (GIC) and Silver GIC (Miracle Mix) using dye penetration technique under stereomicroscope. Forty-five extracted human maxillary central incisors were instrumented and obturated with gutta percha using lateral compaction technique. Following this, the teeth were stored in saline. After one week, teeth were apically resected at an angle of 90ï° to the long axis of the root and root end cavities were prepared. The teeth were divided into three groups of fifteen specimens each and were filled with Group I -MTA, Group II - GIC and Group III - Miracle Mix. The samples were coated with varnish and after drying, they were immersed in 1% methylene blue dye for 72 hours. The teeth were then rinsed, sectioned longitudinally and observed under stereomicroscope. The depth of dye penetration was measured in millimeters. Microleakage was found to be significantly less in MTA (0.83 mm) when compared to GIC (1.32 mm) (p < 0.001) and with Miracle Mix (1.39 mm) (p < 0.001) No significant difference was found when microleakage in Miracle Mix was compared to that of GIC (p = 0.752). Thus we concluded that MTA is a better material as root end filling material to prevent microleakage, in comparison to GIC and Miracle Mix.