The aim of this study was to evaluate in vitro antimicrobial activity of 4 antibiotic agents (for E.faecalis) and 4 antifungal agents (for C.albicans) by agar dilution method. Additionally, modified strip diffusion method was used for detection of in vitro antimicrobial activities of 5% NaOCl, 2.5% NaOCl, 17% EDTA and 2% CHX and agar diffusion method for detection of in vitro susceptibilities of three intracanal medicaments for 18 E.faecalis and 18 C.albicans isolates from primary and secondary root canal infection. Isolates were recovered from 231 endodontic samples of patients, with the need of root canal treatment and retreatment. All tested E.faecalis isolates showed resistance to antibiotics. For irrigation solutions, 2% CHX was more effective in eliminating E.faecalis but 5% NaOCl showed larger inhibition zone than 2.5% NaOCl, 17% EDTA and 2% CHX. For intracanal medication, Ca(OH)2-CHX worked efficiently in killing E.faecalis isolates compared to Ca(OH)2-Steril saline solution, Ca(OH)2-Glycerin. For C.albicans, 18 isolates were susceptible to amphotericin B, nistatin, fluconazole but showed resistance to ketoconazole. 5% NaOCl was more effective in eliminating and produced larger inhibition zone compared to 2.5% NaOCl, 17% EDTA and 2% CHX. Ca(OH)2-Glycerin intracanal medication was better in eliminating C.albicans isolates and produced larger inhibition zone compared to other Ca(OH)2 medicaments.