There is general awareness of artificial selection and its potential implications on health and welfare of animals. Despite growing popularity and increasing numbers of breeds of atypical colour and pattern variants in reptiles, only few studies have investigated the appearance and cause of various diseases associated with colour morphs. Ball pythons (Python regius) are among the most frequently bred reptiles and breeders selected for a multitude of different colour and pattern morphs. Among those colour variants, the spider morph of the ball python is frequently associated with the wobble syndrome. The aim of this study was to determine, whether a morphological variant can be found and brought in association with the clinical occurrence of the wobble syndrome in spider ball pythons, using MRI and CT-imaging as intra-vitam diagnostic methods. Data from eight ball pythons including five spider ball pythons and three wild type ball pythons was assessed and evaluated comparatively. We were able to identify distinctive structural differences in inner ear morphology in spider ball pythons highly probable to relate to the wobble syndrome. To our knowledge, these anomalies are described for the first time and represent a basis for further anatomical and genetic studies and discussions regarding animal welfare in reptile breeding.