The aim of this study was to compare the effect of acidic environment on the dislodgement resistance of mineral trioxide aggregate (MTA) and Bioaggregate (Innovative BioCeramix, Vancouver, Canada) when used as perforation repair materials.Eighty, human, mandibular molars were used. Perforations were made in the furcation of each molar and enlarged to #4 Pesso drills. After perforation repair, specimens of each material were randomly divided into 4 groups (n = 10) according to storage media and time: group A: phosphate-buffered saline (PBS) (pH = 7.4) for 4 days, group B: acetic acid (pH = 5.4) for 4 days, group C: PBS for 34 days, and group D: acetic acid (pH = 5.4) for 4 days followed by exposure to PBS for 30 days. Dislodgment resistance was then measured using a universal testing machine, and then the specimens were vertically split to examine the perforated dentin wall using scanning electron microscopy.MTA resisted dislodgement more efficiently than BA after 4 days in PBS (P < .05). The dislodgment resistance of MTA was significantly reduced (P < .05) after exposure to acetic acid, whereas BA was not affected (P > .05). There was an increase in the dislodgment resistance with the increase in the storage time to 34 days (P < .01). After 34 days, there was a statistically significant difference among groups; the MTA D group had significantly the highest bond strength, and the BA D group D had the lowest (P < .05).MTA is more influenced by acidic pH than BA. Storage for 30 days in PBS can reverse the affected bond of MTA by the acidic environment.