Aim: To investigate the differences in cortisol and melatonin concentrations between children with frequent episodic tension-type headache (FETTH) and healthy children. Methods: Forty-four children, 12 boys/32 girls (age: 9 +/- 2 years) with FETTH associated to peri-cranial tenderness and 44 age-and sex-matched healthy children participated. Both salivary cortisol and melatonin concentrations were collected from non-stimulated saliva following standardized guidelines. A headache diary for 4 weeks was used for collecting intensity, frequency and duration of headache. Results: No significant differences for cortisol (t = -0.431; p = 0.668), and melatonin (z = -1.564; p = 0.118) concentrations and salivary flow rate (z = -1.190; p = 0.234) were found between both groups. No significant effect of age or gender was found. In addition, no significant association between cortisol-melatonin concentrations and between cortisol-melatonin concentrations and headache clinical parameters were found. Conclusion: These results suggest that children with FETTH, at first instance, do not present deficits in the secretion of these cortisol and melatonin. Prospective longitudinal studies are needed to further elucidate the direction of current findings, particularly the synchronism of cortisol and melatonin and the course of the headache.