An infant with multiple joint ankyloses, facial anomalies, and pulmonary hypoplasia, features similar to the phenotype of Pena-Shokeir syndrome, was examined at autopsy. Histological examination of the skeletal muscles revealed many small muscle fibers in a mixed, not group, distribution, although the structure of them was normally arranged. Histochemical assessment of adenosine triphosphatase (ATPase) activity of the iliopsoas muscle demonstrated the failure of the differentiation into type I fibers and the retardation of the skeletal muscle. At the same time, severe pulmonary hypoplasia, which was the likely cause for the retardation of the respiratory system, was found. In contrast to these numerous pathologic changes in the skeletal muscles, no significant abnormalities were observed in the central nervous system except for a somewhat immature external appearance; however, an examination of the spinal cord could not be carried out. Overall, this pattern of pathology suggests the possibility that developmental disorders of the mesenchyme are the primary contributors to the pathogenesis of Pena-Shokeir syndrome, while the immaturity of the central nervous system is involved to a lesser degree.