A 2-day old newborn male, with an uneventful pregnancy and delivery, presented with lethargy, poor feeding, tachycardia, and tachypnea. A sepsis workup was negative. However, venous blood gas demonstrated severe metabolic acidosis with a pH of 7.04 and bicarbonate level of 4 mM/L. Further metabolic workup revealed severe hyperammonemia (687 microM/L) with a normal lactate level (1.5 mM/L). Despite urgent medical treatment by sodium benzoate, arginine, carnitine as well as caloric supplementation, ammonia levels increased within hours to 987 microM/L at the end of the medication loading doses and renal replacement therapy was required. Ammonia clearance by intermittent hemodialysis may be associated with a rapid rebound secondary to redistribution of ammonia. Also, hemodynamic instability secondary to metabolic disease and small patient size makes traditional hemodialysis a less favourable treatment option. Therefore, continuous venous-venous hemodialysis (CVVHD) was initiated. As systemic anticoagulation was deemed dangerous due to a concern of bleeding, regional low dose citrate anticoagulation was used as an alternative to systemic heparinization. More than ten times standard dialysate rate was used to allow efficient clearance of ammonia. Under high flow CVVHD, the patient`s ammonia level declined from the peak level of 1120 microM/L, to under 400 in four 4 hours and under 100 microM/L within 28 hours. Following metabolic assays showed that the patient has methylmalonic acidemia. High flow CRRT using citrate anticoagulation is an effective and relatively safe method to treat severe hyperammonemia. A protocol of using this modality for this indication is proposed.