In a follow-up study of 259 floppy infants of undetermined cause in my laboratory, 11 patients were later diagnosed as having the Prader-Willi syndrome (PWS). To clarify the pathogenesis of muscle hypotonia in PWS, I examined muscle biopsies by histochemical and morphometric methods and the results were compared with those obtained from floppy infants with only mental retardation but with no other features. The histochemical abnormalities of PWS included (i) fiber size variation of both type 1 and 2 fibers, (ii) type 2 fiber atrophy, (iii) increased numbers of type 2C fibers, and (iv) decreased numbers of type 2B fiber. Although muscle hypotonia in PWS has been thought to be due to central nervous system abnormality, my findings suggest that primary muscle pathology, including muscle fiber immaturity and abnormal muscle fiber type distribution, at least in part, plays a role in muscle hypotonia and weakness.