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Background Appropriate and timely diagnosis is one of the most important milestones in effective migraine care and is affected by public awareness, access to medical care, health care systems, and physicians’ knowledge. We assessed the variability in migraine diagnosis rates in different communities under universal national health coverage in Israel. Methods In this population-based retrospective, observational, cohort study, adult (≥18 years) migraine patients were identified in the computerized database of the southern district of the Clalit Health Services Health Maintenance Organization (HMO) based on recorded diagnosis and/or purchase of specific anti-migraine acute medication (triptans). Migraine prevalence in 2018 was calculated in the entire study population and in different municipalities. We utilized a standardized (age and gender) mortality ratio (SMR) approach for comparison among the municipalities. Results In 2018, a total of 29,938 migraine patients were identified out of 391,528 adult HMO members, with an overall prevalence (per 10,000) of migraine of 764.64 (7.65%), 1143.34 (11.43%) for women, and 374.97 (3.75%) for men. Among the municipalities, adjusted prevalence (per 10,000) ranged from 386.15 (3.86%) to 1320.60 (13.21%). The female-to-male ratio ranged from 1.8:1 to 5.1:1. Prevalence rates were positively associated with the socioeconomic status of the municipalities (Spearman rho = 0.472, P = 0.031). Conclusions High variability in the prevalence of diagnosed migraine suggests underdiagnosis. Resources for awareness and educational programs should be directed to low diagnosed prevalence communities. Graphical Abstract