Background. Hyperammonemia caused by ornithine transcarbamylase (OTC) deficiency can be properly managed by continuous arteriovenous hemodiafiltration (CAVHDF). Removal of amino acids (AA) during CAVHDF has not been thoroughly investigated. AA losses in patients with urea cycle defects due to ornithine transcarbamylase deficiency treated by CAVHDF were analyzed. Methods. Twelve neonates with elevated serum ammonia levels, confirmed through urine organic acid analysis and serum amino acid studies, were documented to have OTC deficiency. CAVHDF was administered in an attempt to lower serum ammonia concentration. Amino acid analysis of ultrafiltration and serum were performed by liquid chromatography. Results. Serum levels of leucine, isoleucine, methionine, phenylalanine, and tyrosine were significantly lower than acceptable in these patients. Glutamine was the only amino acid that increased significantly, which is clinically relevant to OTC enzyme deficiency. Although the mean serum concentrations of tyrosine and glutamine concentrations were lower in the dialysate, the serum and dialysate concentrations of other amino acids did not differ. Conclusion. CAVHDF may induce changes in amino acid metabolism and distribution as well. The requirement of aminogram monitor for amino acid supplementation in urea cycle defect patients is important.