The aim of this study was to compare three different cone-beam CT (CBCT) instruments used in dental clinical practice with micro-CT as gold standard. Three female monkeys' (Macaca fascicularis) skulls were selected and scanned by the tested CBCT-s. The most apical visible root canal level on the CBCT images was used as reference level (RL). After the image acquisition by CBCT-s dental jaw sections were scanned by micro-CT at a resolution of 17 µm. Out of the left second and third molars 25 root canals were selected and analysed by three observers at RL and following cross sectional parameters were determined: area of the lumen, major and minor diameters, aspect ratio and mean thickness. Results suggest that only high resolution CBCT instruments allow dentists detecting the full length of the root canal.