Background New clinical oriented approaches are supported by the integration of advanced imaging techniques, e.g. computed tomography and magnetic resonance, with gross anatomy imaging. The interscapular region of the cat is a typical site of a highly invasive infiltrative pathology, i.e. Feline Injection-Site Sarcoma. Even if chemotherapy and radiotherapy have been considered as pre-surgical therapies, extensive surgery is still the recommended treatment. Evidence suggested that the relationships between muscles, infiltrative mass and adjacent musculoskeletal structures could change according to the forelimb positions: a fact to be duly considered while planning the surgical approach. Anatomic and tomographic atlases provide only images of the interscapular region from cats positioned with their forelimbs extended cranially, which means that, they do not record musculoskeletal modifications due to the forelimb movements. Aim of this study was to provide detailed images of the changes occurring in the musculoskeletal structures of the interscapular region of cats according to their forelimb position by comparing cross-sectional gross anatomy, computed tomography and magnetic resonance imaging. Results We provide an atlas of normal cross-sectional anatomy, computed tomography and magnetic resonance imaging of the interscapular region of the cat, from the fifth cervical vertebra to the fifth thoracic vertebra. We compare and couple the slices obtained both in flexed and extended forelimb positioning with the animal maintained in sternal recumbency. Conclusion This study shows a new and dynamic way to investigate the interscapular region of the cat and provides anatomical references for in vivo computed tomography and magnetic resonance imaging, considering changes in the muscular form according to the forelimb positioning. We believe that an in-depth anatomical knowledge of the interscapular region may be helpful to approach the study of any pathology located there and, in particular, to set up an appropriate therapy for the feline injection-site sarcoma.