The accumulation of toxic metabolites in children with inborn errors of metabolism may cause acute metabolic crises and result in long-term neurological dysfunction or death. Peritoneal dialysis often provides insufficient clearance to protect against these complications, while intermittent haemodialysis cannot prevent reaccumulation of metabolites between dialysis sessions. We describe the use of continuous venovenous haemofiltration (CVVH) or haemodiafiltration (CVVHD) in three infants with maple syrup urine disease (MSUD) and one child with carbamyl phosphate synthetase (CPS) deficiency. All children with MSUD had a satisfactory reduction in branched-chain amino acids within 24 h of onset of haemofiltration, and are now neurologically normal. The child with CPS deficiency had an ammonia level of < 100 mumol/l within 24 h of onset of therapy, but died 3 days later from unrelated cardiovascular complications. Complications of the therapy included the clotting of one haemofilter and the replacement of two vascular access catheters per patient on average per therapy. Two patients required blood transfusion. We report the successful use of CVVH and CVVHD in the acute management of metabolic crises associated with inborn errors of metabolism, and believe that these may be the optimal techniques for the acute clearance of toxic metabolites.