Introduction: The present study aimed to evaluate the effect of calcium hydroxide and the modified triple antibiotic paste (MTAP) as intracanal medication on the elimination of the Enterococcus faecalis in retreatment cases. Methods: Sixty patients who attended the outpatient endodontic clinic, faculty of oral and dental medicine, Cairo University were included in this research. Inclusion was limited to patients with symptomatic root canal treated teeth. All teeth underwent non-surgical retreatment. After removal of the gutta percha using protaper rotary retreatment files and irrigation with sodium hypochlorite, the canals were dried and one of the studied medicaments was inserted into the canal in a random sequence. The study was divided into 2 equal groups: Calcium Hydroxide group (CH group n=30) and modified triple antibiotic paste group (MTAP group n=30). Before application of the medicament, canals were sampled using paper points and the colony-forming units grown were counted. After 7 days, the medicaments were removed and the same sampling procedure was repeated. Obturation was then carried out. Results: For both groups, significant decrease in the colony forming units (CFU) of the Enterococcus faecalis resulted after material application. There was no significant difference in CFU between CH group and MTAP group after medication application. Conclusions: MTAP application resulted in decreased CFU of Enterococcus faecalis in nonsurgical retreatment endodontic cases. However there was no statistical significant difference between the use of calcium hydroxide and the modified triple antibiotic paste as intracanal medicament.