The aim of this study was to investigate the root canal system morphology by means of a root canal configuration (RCC) classification described with a four-digit system, the physiological foramen geometry and accessory canal frequency and morphology, of 101 mandibular canines (MaCa) of a Swiss-German population by means of micro-computed tomography. Micro-CT examination of the MaCa was performed and the obtained images analyzed with a 3D imaging software. In single-rooted MaCas, the most frequently observed RCCs were 1-1-1/1 (74.5%) and 1-1-1/2 (14.3%). Seven other RCCs were less frequently observed with a frequency from 4.1 to 1.0%. One physiological foramen was observed in 80.6% of the MaCas, two in 16.3%, three in 1.0% and four in 2.0%. Accessory and connecting canals were apparent only in the middle and apical root thirds. Two-rooted MaCas occurred less frequently (n = 3). When one physiological foramen was present, the mean size of the narrow and wide diameters were 0.28 mm (± 0.07) and 0.40 mm (± 0.11), while the distance between physiological and anatomical foramen was 0.45 mm (± 0.17). MaCas are predominantly single-rooted teeth with a 1-1-1/1 or 1-1-1/2 RCC. Most MaCas had one physiological foramen with an oval shape.