Short stature is a prevalent clinical manifestation in children. While certain causes of short stature can be readily identifiable through routine biological tests, often physicians struggle to ascertain any underlying pathogenic cause, resulting in the diagnosis of idiopathic short stature (ISS). Aggrecan, encoded by ACAN, plays a crucial role in cartilage function and bone growth. The aim of our study is to establish a genotype-phenotype correlation in 24 patients carrying distinct ACAN variants. We conducted a panel-based analysis, including 82 genes associated with genetic skeletal disorders and/or short stature, in 388 French patients who consulted for short stature and/or or skeletal features. Genotype-phenotype correlation analysis was performed for all included subjects. Of all positive patients, 24 (≃20%) were found to carry pathogenic or likely pathogenic ACAN variants distributed across the gene, 20 of which had not been previously reported. We report 23 heterozygous cases and one original case with a homozygous SNV. Two patients harboured the same novel nonsense variant, yet exhibited different phenotypes. Familial studies performed in 21 families demonstrated that ACAN variants were inherited in 20 cases. The cohort demonstrated marked phenotypic heterogeneity, even among affected members within the same family. Radiological skeletal abnormalities were observed in 66% of patients. A comprehensive genomic approach is crucial to identify the true proportion of ISS with a monogenic condition. Our results expand the number of pathogenic ACAN variants with their associated phenotypic spectrum. Aggrecanopathies are heterogeneous and particularly frequent in apparently ISS, even without overt skeletal dysplasia.