To study the purported role of central monoamine disturbances in the pathophysiology of the opsoclonus‐myoclonus syndrome, the serotonin metabolite 5‐hydroxyindoleacetic acid and the dopamine metabolite homovanillic acid were measured in cerebrospinal fluid samples from 27 affected children and 47 age‐ and gender‐matched control subjects by high‐pressure liquid chromatography with elecrochemical detection. 5‐Hydroxyindoleacetic acid and homovanillic acid concentrations in the cerebrospinal fluid were approximately 30 to 40% lower in opsoclonus‐myoclonus patients compared to control subjects, and the normal inverse correlation between age and monoamine metabolite concentrations in the cerebrospinal fluid of control subjects was not found in opsoclonus‐myoclonus patients. Patients with the lowest values were less than 4 years old, and a subgroup had extremely low levels, but differences in older children were not significant. Cerebrospinal fluid levels of 5‐hydroxyindoleacetic acid and homovanillic acid were more positively correlated in control subjects than in opsoclonus‐myoclonus patients. None of the patients exhibited high levels of monoamine metabolites. Homovanillic acid levels were slightly lower in the cerebrospinal fluid of patients receiving corticotropin or steroids at the time of lumbar puncture. Clinical variables that could be excluded were paraneoplastic etiology, anesthetic for lumbar puncture, syndrome duration, age at onset, gender, response to steroids, length of time until initiation of corticotropin or steroids, presence of seizures, opsoclonus, and functional impairment. These data suggest a disturbance and possible altered ontogeny of serotonin or dopamine neurotransmission in a subpopulation of children with opsoclonus‐myoclonus with low cerebrospinal fluid levels of 5‐hydroxyindoleacetic acid and homovanillic acid. Biochemical heterogeneity for this clinical phenotype may have implications for responsiveness to treatment with serotonergic and other drugs.