The purpose of this study was to examine the incidence of root canals with ramifications and accessory root canals close to the apical area of the palatal root of maxillary first molars, and to classify them based on morphology. Using Micro-CT, we created images of 90 extracted Japanese maxillary first molars that were free of caries and other anatomical defects, and conducted three-dimensional observation and measurements in order to classify root canals with ramifications and accessory root canals. None of the root canals in palatal roots of maxillary first molars were completely separated, and all of them were single canals. As for the incidence of root canals with ramification, we found that Type I-a, in which there were no accessory root canals, comprised 65.6 %, while Type I-b, which showed apical ramifications, comprised 31.1 %, and Type I-c, which had lateral canals, comprised 3.3 %. Observation of the cross-section morphology of the root canals revealed strong buccolingual constriction at the root canal orifice, but other than that, the canals had an elliptical shape with a large mesiodistal width. Maxillary first molar palatal roots contain single canals, but strong constriction is observed at the root canal orifice, and accessory root canals are frequently observed in the apical area. These findings indicate the necessity for adequate mechanical and chemical enlargement of the root canal and orifice.