Objectives: The aim of this study is to compare the anti -inflammatory and the anti-microbial effect of the Matricaria chamomilla Fam. Astraceae and the Trigonella foenum-graecum L. Fam. Leguminosae . And to determine their effect on smear layer when used as root canal irrigants. Material and methods: The seeds of Trigonella foenum-graecum L. and flower heads of Matricaria chamomilla L. were percolated in ethanol (70%) till exhaustion to get different fractions. These fractions then were subjected to activity -guided fractionation of plant extracts. Total extract, Petroleum ether, chloroform, ethyl acetate, and the butanol fractions were subjected to anti-inflammatory activity and the antimicrobial test against Staphylococcus aureus and Enterococcus faecalis. The anti-inflammatory activity was carried out following the method of (Domenjoz 1952). For the antimicrobial test The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) were determined by micro broth dilution technique. Results: According to the anti-inflammatory and the antimicrobial tests and as we depend to a greater extent on the antimicrobial effect in the endodontic treatment so the ethyl acetate fraction of Trigonella foenum-graecum L. and the total extract fraction of Matricaria chamomilla L. (most potent fractions) were chosen to be used as a natural irrigants which were used for the smear layer test during the endodontic treatment in teeth. For the smear layer test eighty freshly-extracted, single-canalled, human teeth with straight, completely-formed roots were used for this study. All samples were instrumented by the crown down technique. By examination of the samples under the scanning electron microscope for debris and smear layer removal with a magnification 2000X . The results of the present study revealed the following: In comparison between all groups there was no statistically significantly different between mean smear layer scores at the apical segment. At the middle segment, CHX showed the statistically significantly highest mean smear layer. This was followed by CHX +Fenugreek. There was no statistically significant difference between NaOCL+Fenugreek and Fenugreek. This was followed by CHX+ Chamomile.There was no statistically significant difference between NaOCl, NaOCl +Chamomile, and Chamomile; all showed the statistically significantly lowest mean smear layer % values. At the coronal segment, there was no statistically significant difference between all groups. Conclusion: We can use total extract of Matricaria chamomilla L. and ethyl acetate of Trigonella foenum-graecum L. fractions as irrigants during the root canal treatment for their anti inflammatory and anti microbial effects and benefits. The Matricaria chamomilla fraction 2% could be used instead of sodium hypochlorite as a natural irrigant in the root canal due to its effect on the smear layer removal as it showed higher effect than the sodium hypochlorite.