Pompe disease, a disorder caused by a deficiency in the lysosomal enzyme acid alpha glucosidase, is frequently overlooked as a cause of floppy baby syndrome. The accurate diagnosis of floppy baby syndrome requires the sequential evaluation of medical causes (e.g., hypothyroidism, sepsis, malnutrition, malabsorption, congenital heart disease), neurologic etiologies (central [cerebral] and peripheral [lower motor unit]) and anatomic characteristics of the abnormality. Cardiomegaly on chest x-ray in a patient with floppy baby syndrome should alert the pediatrician to suspect Pompe disease. Based on this finding, further work-up or referral to a specialist can be considered. Pompe disease requires immediate attention. Symptomatic intervention of this disorder should be initiated at the earliest time possible to maximize the potential benefit from therapy and to prevent irreversible organ damage. Moreover, early diagnosis is important for providing parents with realistic information about their child's prognosis, and where appropriate, professional genetic counseling. Enzyme replacement therapy (ERT) with recombinant human GAA is currently being evaluated in clinical trials; the future availability of this option makes early identification of this condition even more critical. This article presents a unified view on the optimal approach to the accurate diagnosis of Pompe disease and to its recognition as one of the possible and treatable causes of floppy baby syndrome.