Background: To determine the clinical relevance of change in the level of lactate in the serum as a meanings of establishing the efficacy of the circulation immediately after the Fontan procedure in small children. Methods: We measured the concentration of lactate in the serum consecutively in 30 patients undergoing the Fontan procedure, without fenestration, under the age of 2 years. Of these, we did not use cardiopulmonary bypass in 13. Results: Concentrations gradually increased during the first several hours after establishment of the Fontan circulation, and then eventually decreased, reaching the normal range within 48 hours, with specific values of 0.9 plus or minus 0.3 pre-operatively, 2.3 plus or minus 1.1 immediately after creation of the Fontan circulation, 4.0 plus or minus 2.4 at 6 hours, 1.6 plus or minus 0.6 at 24 hours, and finally 1.3 plus or minus 0.4 millimoles per litre at 48 hours. This trend was irrespective of use or no use of cardiopulmonary bypass. The higher initial level in the intensive care unit was related to higher systemic venous pressure, higher transpulmonary pressure gradient, higher maximal level of alanine transaminase and blood urea nitrogen, and longer duration of peritoneal drainage, the latter as a monitor of sequestration of fluid rather than peritoneal dialysis. In patients with initial levels greater than 3.0 millimoles per litre, there was extended duration of endotracheal intubation. Conclusions: Postoperative changes in the levels of lactate in the serum subsequent to creation of the Fontan procedure were peculiar, not necessarily correlated with the cardiac output, but relevant to the clinical course.