The bidirectional Glenn and Fontan procedures are empirically performed as interim and definitive procedures in children with a functionally single ventricle. The optimal stage of palliation, nonetheless, remains unknown. During childhood, growth is a fundamental measure of response to therapy. Growth may be influenced by the degree of cyanosis, the volume load on the ventricle, and cardiac performance. Thus, the weight and stature of children with a functionally single ventricle who underwent a bidirectional Glenn procedure or a Fontan procedure were studied to determine the effect of each intervention on growth. Z scores for weight and stature were retrospectively determined prior to palliation, at yearly intervals for 4 years, and from long-term measurements until 18 years of age in all patients with at least 2 years of observation following palliation. Growth was evaluated in 54 patients with a bidirectional Glenn procedure, and 65 patients with a Fontan procedure. The Z scores for weight were improved after each method of surgical palliation. Stature, however, was improved only following the bidirectional Glenn procedure. Growth was impaired in patients who developed protein losing enteropathy. Weight improved only during the initial 2 years after the Fontan procedure in patients who had a surgical fenestration. Over the long-term, patients who underwent a Fontan procedure were more likely to have a Z score less than −2.0 for weight and stature than patients who underwent only a bidirectional Glenn procedure. Late mortality and the incidence of heart transplantation were increased in patients who experienced a decrease in their rate of growth, defined as a negative change of more than one Z score in weight or stature, following the Fontan procedure. In conclusion, at moderately increased altitude, children with a functionally single ventricle grow more appropriately following the bidirectional Glenn procedure than following the Fontan procedure. A decrease in the rate of growth is associated with a poor prognosis following the Fontan procedure.