Objectives: To assess the presence, prevalence and clinical characteristics of primary headaches in pediatric patients with chronic rheumatic diseases such as juvenile idiopathic arthritis (JIA) and familial Mediterranean fever (FMF), and to analyze the common pathophysiological mechanisms. Study design: In this noncontrolled, cross-sectional study, a semi-structured 53 item headache questionnaire was administered to subjects with FMF and JIA, and interviewed a total sample size of 601 patients younger than 16 years of age. The questionnaires were then analyzed according to the International Headache Society's diagnostic criteria. Results: Children with FMF (n = 378) and JIA (n = 223) were studied. Each group was then divided into two subgroups according to whether the subjects reported headache or not. 29.5% of subjects with FMF reported having migraine, 37.6% probable migraine and 32.9% tension type headache (TTH). In JIA group 28.2% were diagnosed with migraine; 41.2% with probable migraine and 30.6% with TTH. No significant difference was found between all subjects with (n = 258) and without (n = 343) headache for variables such as living in a crowded family (p = 0.95), being the first child in the family (p = 0.63), academic achievement of the child (p = 0.63), high education level (higher than high school) of the mother (p = 0.52) and father (p = 0.46), The presence of systemic disease was reported not to be effecting the daily life at the time of evaluation by 90.2% of the children with headache and 91.0% of the children without headache (p = 0.94). 81.4% of the children reported their headaches were not aggravating with the exacerbation periods of their systemic disease. Family history of hypertension was reported higher by the subjects with headache (13.5% with headache and 4.0% without headache p = 0.001). Diabetes mellitus was also reported higher (5.8% with headache; 0.5% without headache; p = 0.006) Family history of headache was reported in 28.2% of the patients with headache whereas it was 17.4% of the patients without headache (p < 0.001). Family history of headache was reported in 28.2% of the FMF subjects with headache whereas it was 17.4% of the patients without headache (p < 0.001). For JIA patients a positive family history for headache was obtained in 25.9% of children with headache notably in migraineurs (81.8%). Conclusion: Patients with JIA and FMF should be asked specifically about accompanying primary headaches particularly migraine headaches as they may be additional disabilities for these patients. (C) 2014 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.