Current imaging methods in pre-clinical and animal model studies of penile disease are limited because of the small penis of a rat – standard laboratory animal used in this type of research. Routine visualization methods of surface and inner structures of the penis used in clinical medicine are not suitable in experimental animal researches. The only method available for these purposes is histopathological analysis, which does not provide complex view on penile structures due to two-dimensional imaging per slide. In the pre study we evaluated and compared capability of ultrasound, histopathological and micro-computed tomography imaging methods to visualize anatomical structures of laboratory rabbit penis. Ultrasound provides limited imaging in comparison with other methods. However, it could be useful in assessment rough structural alterations of tunica albuginea and corpora cavernosa as a secondary and supportive method. Micro computed tomography provides nearly the same image quality as histopathological analysis. Moreover, it gives a complex view on the whole penile sample due to three-dimensional reconstruction. This fact gives reason to use this method as a basic one in the pre-clinical trials and animal model studies.