Limited information about the skeletal anatomical features of the European pond turtle (Emys orbicularis), one of the species of turtles in Iran, is available. Given that performing clinical examinations as well using imaging techniques require complete anatomical information of the animal, it is essential to study these features in various researches. This study was done to provide complete anatomical information of the vertebrae and different shell parts in European pond turtles, as well as their normal three-dimensional computed tomographic (3D CT)-Scan images in both flexed and extended neck positions. This study was performed on 10 European pond turtles. CT-Scan images were taken from each sample and in the 3D reconstruction of the images, different patterns were used. 8 cervical vertebrae, 10 dorsal vertebrae, 2 sacral vertebrae, and 25 caudal vertebrae were observed in European pond turtles. The cervical vertebrae were highly mobile and there were no cervical ribs. Due to the fusion of the dorsal vertebrae, there were no intervertebral foramina in this section, but very small lateral vertebral foramina were visible. These foramina were formed in the last four dorsal vertebrae at the fusion site and they were larger than the foramina of the cranial vertebrae. According to the results of this study, it can be concluded that the use of diagnostic techniques such as a 3D CT-Scan is very useful in the study of skeletons. The correct direction and position of the bones can be easily determined using this technique. Part of the turtle`s ability to contract the neck is due to the special structure of the articular processes of the last two cervical vertebrae and the first dorsal vertebra. One of the most important adaptations in the evolution of the special structure of the seventh and eighth vertebrae of the neck and the way they are articulated.