Abstract Background Dachshunds have a high prevalence of intervertebral disc disease (IVDD) to which they are predisposed due to early intervertebral disc (IVD) degeneration and calcification. Moreover, the recently found 12-FGF4 retrogene (RG) is associated with calcified discs visible on radiographs (CDVR) and IVDD. Earlier studies suggest that all IVDs of one-year-old Dachshunds show signs of degeneration. This prospective, analytical, blinded study aimed to investigate the extent and distribution of IVD degeneration in young adult (24–31 months) asymptomatic Dachshunds (n = 21) hypothesizing that not all IVDs of two-year-old Dachshunds are degenerated. Another aim was to explore the correlations between IVD degeneration evaluated with magnetic resonance imaging (MRI), the number of CDVR, and the dog’s 12-FGF4RG status. The study protocol included grading the CDVR on spinal radiographs, grading the IVD degeneration on T2-weighted sagittal and transverse high-field MR images of all IVDs (n = 546), and 12-FGF4RG variant genotyping. Results Of all IVDs evaluated, 2% (n = 11) were normal based on MRI grading. Despite the study population having moderately degenerated IVDs (median MRI grade 3), there was also variation in the degree of IVD degeneration between individuals and in the distribution of IVD degeneration between different vertebral regions. The number of CDVR correlated significantly with the magnitude of IVD degeneration based on MRI evaluation and with the 12-FGF4RG genotype. The odds for being 12-FGF4RG homozygous were higher for Dachshunds with CDVR. However, the 12-FGF4RG variant did not alone explain the phenotypic variation in IVD degeneration. Conclusions The number of CDVR is a valid indicator of overall IVD degeneration, as it correlates with MRI-based IVD grading. Also, as the extent and distribution of IVD degeneration varies between individual Dachshunds, selective breeding against IVDD using radiographic screening and 12-FGF4RG variant genotyping is possible.