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Objectives: The aim of this study was to evaluate the performance of different analytic methods, such as liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), high-performance liquid chromatography-ultraviolet (HPLC-UV), enzyme-linked immunosorbent assay (EIA), and chemiluminescence immunoassays (CLIA), in order to highlight whether or not there is relative superiority amongst the assays. We analyzed two groups of subjects suffering from headache and two groups of healthy subjects. Design and Methods: We performed a prospective, single-blind single-center control-group study on 220 subjects with migraine. Subjects of both sexes >10 years old and with 12 months' history of migraine were eligible for the study. As a control group, 120 healthy subjects were chosen by their family physician. Results: LC-MS/MS evaluation documented that in all enrolled subjects (migraine and control groups), the serum vitamin D3 levels were lower with respect to the normal range (30–100 ng/mL), with a mean value of 15.4 ng/mL, without difference between sex. The mean values measured using HPLC-UV, EIA, and CLIA tests such as Liaison® and Architect® did not show significant differences compared to the values obtained using LC-MS/MS. Conclusions: In conclusion, the population generally has low values of the vitamin D3 hormone, and the suggested range should probably be revised. HPLC-UV and CLIA were found to have appropriate analytical values compared to the reference method (LC-MS/MS), so it is possible to suggest their routine use to optimize care. [ABSTRACT FROM AUTHOR]