INTRODUCTION: This study aimed to compare the thickness of the mesiobuccal furcal canal walls of first and second maxillary molars. MATERIALS AND METHODS: This study was performed on total of 30 first and second extracted molar teeth (15 each). The mesiobuccal roots of each tooth were separated at the cement-enamel junction (CEJ) level and embedded in acrylic resin. The embedded roots were cut horizontally at two and four mm below the CEJ using a 0.20 mm blade (overall three sections CEJ, two and four mm below). Next, photographs of all the horizontal sections were taken using a digital stereomicroscope with identical magnifications (×20). Using the photographs, two independent observers measured and recorded the minimal thickness from the canal wall of the first mesiobuccal (MB1) and the second mesiobuccal (MB2) canals to the furcation area. Data analysis was performed by repeating the measurement Analysis of Variance. The analysis was completed by making paired comparisons using the Bonferroni alpha adjustment method. Statistical significance was set at P<0.05. RESULTS: In maxillary first molars, the mean (±SD) thickness of the canal furcal wall MB1 in three sections were significantly higher than thickness of the canal furcal wall in MB2 (P<0.05). However there was no statistical difference between the mean (±SD) thickness of the canal furcal wall in the three sections (CEJ, 2 and 4 mm below) of maxillary second molars MB1 and MB2 canals. CONCLUSION: Only the maxillary first molars demonstrated significantly lower furcal canal wall thickness (FCWT) values in the MB2 canals. Maxillary second molars MB canals did not demonstrate statistical difference in FCWT values.