We have previously examined the clinical manifestations, treatments and prognosis of 177 patients with urea cycle disorders (UCDs) from January 1999 to March 2009 in Japan. In this study, we investigated the incidence of clinical manifestations in different peak blood ammonia level at onset in UCD patients, and examined the growth of OTCD (ornithine transcarbamylase deficiency) patients. The UCD patients who had a high peak blood ammonia level at onset showed significantly high incidence of convulsion and abnormal head computed tomography or magnetic resonance imaging. The patients also showed significantly high incidence of hemodialysis and liver transplantation. Choice of therapeutic agents for long-term treatment is not different between peak blood ammonia levels at the onset, except for the use of special amino-acid formulas. Growth retardation is not affected by high peak blood ammonia level at onset; however, 32% of male and 52% of female OTCD patients over 1 year old were plotted under the 10th percentile, and showed growth failure. The final height of the male and female OTCD patients were 166.2±5.5 and 150.3±7.2 cm, respectively. Although the prognosis of UCDs was improved significantly, it is considered that there are still many difficulties in the UCD patient's life.