Molar-incisor malformation (MIM) is a new type of root anomaly reported recently. The characteristics of MIM are dysplastic root formations, constriction of pulp chambers and presence of calcified matrices at the level of cementoenamel junction in permanent first molars and primary second molars. In some cases, permanent maxillary incisors are also affected. The permanent first molars of the patient in this case report were affected with MIM. Generalized pulp stones were observed in overall primary dentition. Micro-computed tomography (micro-CT) imaging and scanning electron microscope-energy dispersive X-ray spectrometer analysis were performed on the extracted mandibular first molar and maxillary primary second molar of the patient. Micro-CT images revealed the discontinuity of enamel directly connected to an accessory canal of the root.