We determined the cerebrospinal fluid (CSF) and serum neuron-specific enolase (NSE) concentrations in 19 patients with acute benign headache. All patients had normal neurological examination, CSF and head computed tomography scan. The final diagnoses were: primary thunderclap headache (n = 7), primary exertional headache (n = 3), primary cough headache (n = 1), migraine without aura (n = 4), headache unspecified (n = 2), probable infrequent episodic tension-type headache (n = 1), headache attributed to hypertensive crisis without hypertensive encephalopathy (n = 1). A group of 108 healthy subjects served as controls. CSF NSE concentration was 14.16 ng/ml [95% confidence interval (CI) 11.86, 16.47)] in the headache sample (controls 17.19 ng/ml, 95% CI 16.23, 18.15). Serum NSE concentration was 7.50 ng/ml (95% CI 5.20, 9.80) in the headache sample (controls 8.45 ng/ml, 95% CI 7.67, 9.23). CSF/serum ratio was 2.81 (95% CI 2.21, 3.40) in the headache sample (controls 2.23, 95% CI 2.03, 2.42). Acute benign headache is not associated with neuronal damage as estimated by means of CSF and serum NSE concentration.