The co-occurrence of skeletal dysplasia and ophthalmologic abnormality is extremely rare. We report on a boy of a unique form of spondylometaphyseal dysplasia associated with cone-rod dystrophy. He presented with postnatal severe short stature, progressive lower limb deformity with rhizomelic shortening of the long bones, prominent joints with limited mobility in knees and elbows, mild thoracic scoliosis, and vision impairment due to cone dystrophy. Correction of deformity and simultaneous limb lengthening was performed in bilateral femora and tibiae without major complications. Skeletal manifestations in addition to comprehensive ophthalmologic examinations were described in this patient who had been followed from infancy to 16 years of age.