Fontan circulation is characterized by many features commonly observed in heart failure that may affect physical growth regardless of pituitary gland dysfunction status. The aims of the present study were to investigate the prevalence of short stature and growth hormone deficiency (GHD) and determine the factors associated with short stature after Fontan surgery. On retrospective evaluation of 47 patients after Fontan surgery, a very high prevalence of short stature was observed (38.3%). In the short stature group, 5 patients were diagnosed with GHD (10.6% of patients after Fontan Surgery), which is much higher than the frequency of 1/10,000 in the general population. Central venous pressure (CVP) was significantly higher (14.6±4.5 vs. 12.2±1.9 mmHg, P<0.05) and the blood pressure and arterial oxygen saturation were significantly lower in the short stature group. Laboratory data also indicated volume retention and congestion in the short stature group. Mean change in stature from catheterization 1 year after Fontan surgery to the most recent visit was significantly lower in the short stature group (-1.1±1.1 SD vs. 0.0±0.8 SD, P<0.05) and significantly negatively correlated with CVP (r=-0.42, P<0.05). Volume retention and congestion, the prominent features of Fontan circulation, affect physical growth partly due to pituitary gland dysfunction, highlighting the need for the screening for and treatment of this condition after Fontan surgery.