Introduction: It is still not clear what specific value of hyperammonemia causes brain damage in critical patients, specifically in patients diagnosed with hypoxic-ischemic encephalopathy.Objective: To evaluate ammonium levels in neonates diagnosed with hypoxic-ischemic encephalopathy subjected to hypothermic therapy and their relation to the other variables in hypoperfusion.Methodology: Analytic observational study of neonates diagnosed with hypoxic-ischemic encephalopathy treated with cerebral hypothermia in which blood ammonium levels were compared to other hypoperfusion variables such as Ph, base excess, magnesium, lactate, and with the presence of seizures and death to determine whether a correlation existed. Results:The average serum ammonium level was 57.45µmol/lt, and there were only two patients with ammonium levels above 110µmol/lt.Most patients had seizures and four patients died.There was no correlation found between ammonium and the other hypoperfusion variables, with values of R2< 0.1.Neither was a correlation found between the presence of seizures and death (R2 0.203 and 0.005 respectively). Conclusion:In neonates diagnosed with hypoxic-ischemic encephalopathy managed with hypothermia, the values for serum ammonium do not correlate to the severity of the encephalopathy for the short-term prognosis.For this reason, it cannot be assumed that hyperammonemia is caused for hypoxia, and it is necessary to look for differential diagnoses for hyperammonemia.