Aim to evaluate antimicrobial efficacy of chamomile and thyme extracts as intra canal irrigants and their effect on the smear layer removal. Methodology Forty recently extracted single rooted permanent teeth with completely formed roots will be collected then stored in normal saline solution at room temperature. The teeth will be divided into control group of ten roots and experimental group of thirty roots. The root canals of thirty roots of the experimental group will be injected by saliva then incubated at 37 degrees in thioglycolate broth for up to 72 hours. The control group consists of ten roots which will be divided into two subgroups of five roots each. The positive control group will be injected by saliva then transferred to thioglycolate broth, while the negative control group will be transferred immediately after autoclaving into thioglycolate broth without saliva or any irrigant. All turbid broth cultures will be subcultured on 2 plates of solid media, one incubated aerobically and the other anaerobically. Direct microscopic examination will be done after gram staining and complete identification of the strains will be done by gram stain results. Then the experimental group of thirty roots will be divided into three equal subgroups of ten roots each: group I : Irrigated with German chamomile group II: Irrigated with Thymus vulgaris group III: Irrigated with soduim hypochlorite All roots will be tranferred into thioglycolate broth and subcultured for proper identification of the strains. Thirty five mandibular and maxillary single rooted non carious teeth with fully developed apices will be divided into 3 groups according to the type of irrigating solution used, 10 teeth each and control group of 5 teeth. Control group: saline solution Group A: chamomile (Marticaria recutita L.) Group B: Thyme (Thymus vulgaris L.) Group C: 2.5 % Sodium hypochlorite + 17 % EDTA After preparation of the root canal, 10 ml final flush with the appropriate irrigant will be carried out. The roots will be split into two halves and prepared to be examined under Scanning Electron Microscope at different magnifications. Results A comparison of the antimicrobial activity among the irrigating solutions revealed that chamomile extract was the most potent antimicrobial agent in comparison with thyme extract and sodium hypochlorite. NaOCl+EDTA was the most effective irrigant in smear layer removal and obtaining clean surface. Conclusions Chamomile was the most potent antimicrobial irrigant and effective in smear layer removal.