Odontogenic lesions such as AB and KOT are benign but have aggressive and invasive behavior with high recurrence rates as well which remains the main obstacle for different treatment modalities. CSCs are a small group of cells that present in many neoplasms and they are responsible for their aggressiveness and relapse after the treatment. The current study evaluated immunohistochemical expression of ABCG2 and CD44 (CSC markers) in AB, ABC, KOT and tooth follicle of permanent teeth. To compare the expression of these two markers and correlate the obtained results with the biological behavior of such lesions. The study was performed using thirty seven archival cases of AB (15 cases), ABC, KOT (10 cases each) and tooth follicle of permanent teeth (2 cases). These cases were stained using H&E for histological examination. Indirect biotin free system/HRP-conjugated secondary antibody was used for immunostaining by anti-ABCG2 and anti-CD44 antibodies. As regard immunohistochemical evaluation, the stained sections were examined by ordinary light microscope. The area percentage of the positive ABCG2 and CD44 immunoreactions was measured by image analyzer computer system using the software Leica Qwin 500. All the obtained data were statistically evaluated; comparisons among the used lesions were done using ANOVA test, this was followed by Tukey’s post hoc test when the difference was found to be significant. Unpaired t test was used to compare the epithelium and connective tissue within the same group. Pearson correlation test was used to study correlation between both markers. The study results revealed that the expression level of ABCG2 was gradually decreased starting form tooth follicle to AB, ABC until reaching the lowest expression in the KOT epithelium. The statistical analysis was extremely significant between all lesions. According to CD44 expression, it was the highest at AB with no statistical significance between AB, ABC and KOT whereas the lowest expression in the tooth follicle. The area percentage of CD44 immunoexpression was much greater that of ABCG2 and the correlation between both markers was weak positive. Summary Finally; it is obvious form the study results that CD44 is more reliable CSC marker for odontogenic lesions used, while ABCG2 have no or a minor role as a CSC marker in the tumorgenesis of such lesions.