Background: Apical leakage assessment is a way to compare the efficiency of a filling material to seal the apical region of the tooth. Many microleakage testing techniques have been introduced through the years, but there has been no agreement as to which technique gives the most accurate results. The aim of this study was to compare the accuracy of fluid filtration and bacterial leakage techniques in the assessment of the apical sealing ability of mineral trioxide aggregate (MTA) and calcium enriched mixture (CEM). Materials and Methods: A sample of 34 extracted single-rooted human teeth were selected and prepared. The samples were divided in to 2 experimental groups. The apical 3 mm of each root was resected at 90° to its long axis and root end preparation was done with ultrasonic tips to a depth of 3 mm and filled with MTA and CEM, respectively. Assessment of apical sealing ability was done with fluid filtration technique and bacterial leakage technique along 90 days with Enterococcus faecalis bacteria. Mann-Whitney U-test and Chi-square test were used to analyze the data using SPSS (SPSS Inc., Chicago, IL, USA). P less than 0.05 was considered as significant. Results: There was no significant difference in apical sealing ability between MTA and CEM in bacterial leakage and fluid filtration techniques. Samples which had bacterial leakage showed higher leakage values by fluid filtration technique. Conclusion: Both techniques showed same results and there was no significant difference between fluid filtration and bacterial leakage techniques in assessment of apical microleakage.