Achondroplasia (ACH) and hypochondroplasia (HCH) share clinical features characterized by disproportionate short stature with rhizomelic shortening of the limbs. In an attempt to clarify genotype-phenotype correlation in ACH and HCH, we investigated the presence of the previously identified mutations of FGFR3 in 26 patients with ACH- or HCH-mimicking features and compared clinical and radiographic findings between the two groups. Using genomic DNA sequencing and RFLP analysis, G380R, an ACH-specific mutation, and N540K, an HCH-specific mutation, were detected in 13 patients (50%) and five patients (19%), respectively. No mutations of FGFR3 were detected in eight patients (31%). No remarkable clinical or radiological differences were evident among the ACH infants and children with G380R, the HCH patients with N540K, and the patients without verified mutations. These results suggest that genotype-based diagnosis needs to precede proper genetic counseling for patients with ACH or HCH, which show very similar clinical and radiological features.