The root canal system morphology of the mandibular second molar was investigated by means of micro-computed tomography. The root canal configuration (RCC), foramina and accessory canals frequency of 93 mandibular second molars of an Egyptian sample were investigatedby micor-CT scans. The RCC and main foramina number (MFN) are described by means of a four-digit system from coronal to apical. The most frequently observed RCCs in the mesial root were 2-2-1/1 (32.3%), 2-2-2/2 (28.0%), 1-1-1/1 (6.5%) and 2-1-1/1 (6.5%); an additional twelve different RCCs were also found here. In the distal root, the RCC 1-1-1/1 was observed in 81.7%; another ten different RCCs with a frequency of less than 5% were also observed in this root. Anastomoses between the mesiobuccal and mesiolingual canals in the mesial root were witnessed in the coronal (20.5%), middle (19.4%) and apical (10.8%) thirds. Accessory canals were found in the coronal (mesiobuccal 15.0%, mesiolingual 12.9%, distobuccal 1.1%), middle (mesiobuccal 7.5%, mesiolingual 10.8%, distolingual 3.3%) and apical (mesiobuccal 19.3%, mesiolingual 16.2%, distolingual 10.8%, distobuccal 2.2%) thirds. The RCC of mandibular second molars showed a great variety. When compared with the first mandibular molar in a historical control from the same sample, the mandibular second molar presented less morphological diversifications. Yet, the mesial root canal system of the mandibular second molar showed more RCC variations, connecting and accessory canals than the distal root.