Early-onset epileptic encephalopathies are devastating conditions. Little is known about pathophysiology and biological markers. We aimed to identify a relationship between the type and prognosis of epileptic encephalopathies starting in infancy and the cerebrospinal fluid profile of pterins and neurotransmitters. Cerebrospinal fluid samples of 23 infants with epileptic encephalopathies were analysed for biogenic amine metabolites (homovanillic and 5-hydroxyindoleacetic acids), and pterins (neopterin and biopterin). West syndrome, early-infantile epileptic encephalopathy with suppression-bursts or Ohtahara syndrome, severe epilepsy with multiple independent spike foci and partial epilepsy with multiple independent spike foci were the four types of epileptic encephalopathy studied. We report clinical, electroencephalographic, neuroimaging and follow-up data. Among the 23 patients studied, 7 had high neopterin levels. Four of them had partial epilepsy with multiple independent spike foci. High neopterin values were associated with mortality (chi square = 7.304, p = 0.007). 5-Hydroxyindoleacetic acid levels were above reference values in three patients, two with partial epilepsy with multiple independent spike foci and one with West syndrome. Homovanillic acid was normal in almost all infants studied. In conclusion, high neopterin levels suggest a cellular immune activation in the central nervous system of these infants, with apparent prognosis implications.