Abstract Background A 20-month-old Asian boy with normal growth presented with genu valgum, kyphosis, and pectus carinatum, with no neurological symptoms. No other symptoms suggestive of mucopolysaccharidoses, for example joint contracture and peculiar facies, were present. Case presentation As part of our differential diagnosis we found elevated urine glycosaminoglycans, which triggered further investigation. Detailed examination showed flattening of the ribs, kyphoscoliosis and ovalization of the thoracolumbar vertebral body, strikingly short metacarpals, and very slight cardiac regurgitation. N-Acetylgalactosamine-6-sulfatase levels in the blood and dermal fibroblasts were very low, thus confirming diagnosis of Morquio A within 2 months of presentation. The patient was placed on elosulfase alfa enzyme replacement therapy and followed for 3 years. Conclusions This case exemplifies the importance of considering mucopolysaccharidoses as part of the initial differential diagnosis of pediatric patients with skeletal deformities; urine glycosaminoglycan levels and a blood enzyme mucopolysaccharidoses panel are simple screening tests that could lead to early definitive diagnosis.