Skeletal dysplasia (SD) is a large and heterogeneous group of rare genetic disorders that affects bone and cartilage growth. These disorders are diagnosed based on radiographic, clinical, and molecular criteria. However, the diagnostics is challenging due to clinical and genetic heterogeneity. We present the experience of systematic use of comprehensive genetic testing in the national health system and the molecular epidemiology of SD in Slovenia.We retrospectively reviewed 470 patients with clinical features of SD, including prenatal, childhood, and adult patients referred for diagnostic genetic evaluation to the national genetic reference center over ten years. In 262 patients, whole exome or whole genome sequencing was performed, while direct gene sequencing was performed in 208 patients with a specific clinical diagnosis.A definitive genetic diagnosis using NGS was achieved in 50% (n=131) of patients. Among the positive cases, 49.61% initially presented with a nonspecific diagnosis of SD, and genetic testing contributed to establishing the diagnosis. Moreover, we demonstrated high genetic heterogeneity in our SD cohort with 66 distinct causative genes, resulting in different types of SD. In detail, we detected 132 causative variants, of which 29 were novel, which expanded the mutational spectrum of SD. Furthermore, pathogenic copy number variants (CNVs) were identified in 4.55% of the total number of variants, highlighting the importance of CNV analysis in expanding the yield of molecular diagnosis of SD.With the systematic use of WES and WGS, we have significantly improved the diagnostic yield of SD in the national health system and access to genetic testing. Moreover, we found significant genetic heterogeneity, and we report the genetic epidemiology of SD in the Slovenian population.