Background Shape of the dental root canal is highly patient specific. Automated identification methods of the medial line of dental root canals and the reproduction of their 3D shape can be beneficial for planning endodontic interventions as severely curved root canals or multi-rooted teeth may pose treatment challenges. Accurate shape information of the root canals may also be used by manufacturers of endodontic instruments in order to make more efficient clinical tools. Method Novel image processing procedures dedicated to the automated detection of the medial axis of the root canal from dental micro-CT and cone-beam CT records are developed. For micro-CT, the 3D model of the root canal is built up from several hundred parallel cross sections, using image enhancement, histogram based fuzzy c-means clustering, center point detection in the segmented slice, three dimensional inner surface reconstruction, and potential field driven curve skeleton extraction in three dimensions. Cone-beam CT records are processed with image enhancement filters and fuzzy chain based regional segmentation, followed by the reconstruction of the root canal surface and detecting its skeleton via a mesh contraction algorithm. Results The proposed medial line identification and root canal detection algorithms are validated on clinical data sets. 25 micro-CT and 36 cone-beam-CT records are used in the validation procedure. The overall success rate of the automatic dental root canal identification was about 92% in both procedures. The algorithms proved to be accurate enough for endodontic therapy planning. Conclusions Accurate medial line identification and shape detection algorithms of dental root canal have been developed. Different procedures are defined for micro-CT and cone-beam CT records. The automated execution of the subsequent processing steps allows easy application of the algorithms in the dental care. The output data of the image processing procedures is suitable for mathematical modeling of the central line. The proposed methods can help automate the preparation and design of several kinds of endodontic interventions.