A well-protected microbial habitat may be present in the root and canal morphology, which is varied and complicated. Before initiating effective root canal treatment, a detailed knowledge of the root and canal anatomical variances in each tooth is a must. This study aimed to investigate the root canal configuration, apical constriction anatomy, location of the apical foramen, dentine thickness, and prevalence of accessory canals in mandibular molar teeth in an Egyptian subpopulation using micro-computed tomography (microCT). A total of 96 mandibular first molars were scanned using microCT, and 3D reconstruction was performed using Mimics software. The root canal configurations of each of the mesial and distal root were classified with two different classification systems. The prevalence and dentin thickness around middle mesial and middle distal canals were investigated. The number, location and anatomy of major apical foramina and the apical constriction anatomy analysed. The number and location of accessory canals were identified. Our findings showed that two separate canals (15%) and one single canal (65%) were the most common configuration in the mesial and distal roots, respectively. More than half of the mesial roots had complex canal configurations and 51% had middle mesial canals. The single apical constriction anatomy was the most common for both canals followed by the parallel anatomy. Disto-lingual and distal locations of the apical foramen are the most common location for both roots. Mandibular molars in Egyptians show a wide range of variations in root canal anatomy with high prevalence of middle mesial canals. Clinicians should be aware of such anatomical variations for successful root canal treatment procedures. A specific access refinement protocol and appropriate shaping parameters should be designated for each case to fulfil the mechanical and biological objectives of root canal treatment without compromising the longevity of treated teeth.