Background: Guinea pig is a species belonging to the Caviidae family of the Rodentia order and is frequently used in experimental studies. Biomedical imaging methods are used in the diagnosis and treatment of many diseases in medicine. Among these methods, computed tomography (CT) is one of the most important imaging methods. In this study, it was aimed to perform the three-dimensional (3D) modelling of the CT images, obtained from the humerus and femur in the Guinea pigs, via the MIMICS programme, and to make some biometric measurements regarding the bones over these models. Materials and methods: In the present study, 12 male adult Guinea pigs were used. The soft tissue on the humerus and femur bones of the Guinea pigs was removed. After this procedure, CT images at a 0.5 mm-thickness were obtained from the animals. The images were recorded in DICOM format. Then, the reconstruction process was performed from the images by using the 3D modelling programme MIMICS® 13.1. On the 3D model of the humerus and femur (right-left), volumes, surface areas and lengths as well as other biometric parameters were measured separately, and the values were recorded. In addition, measurements of the bones were made with the help of a digital calliper. Results: Among the parameters obtained from 3D models, a statistical difference was observed between the right and left cortical thicknesses of the femur from the measurements of calliper and the right and left humerus volumes (p < 0.05); whereas, no statistical difference was found in other parameters of both measurements (p > 0.05). Conclusions: It can be stated that CT and 3D modelling can be used for the measurement of some parameters in the long bones of the Guinea pigs.