Background: The aim of this study was to determine the plasma levels of cyclooxygenase-2 (COX-2) and visfatin in different stages and different subtypes of migraine headaches compared to a control group to elucidate the pathological mechanisms involved. Material/Methods: We recruited a case-control cohort of 182 adult migraine patients and 80 age-matched and gender-matched healthy controls. The migraine patients were divided into two groups: the headache-attack-period group (Group A, n=77) and the headache-free-period group (Group B, n=105). The two groups were further divided into subgroups according to whether they had aura symptoms. Solid phase double antibody sandwich enzyme-linked immunosorbent assay (ELISA) was used to measure the plasma levels of COX-2 and visfatin. Statistical analysis was performed using SPSS 17.0. Results: The plasma levels of COX-2 and visfatin in the headache-attack-period group were significantly higher than in the headache-free-period group and the control group; there were no significant differences between the headache-free group and the control group. There were no significant differences in plasma levels of COX-2 and visfatin between the subgroups: headache-attack-period with aura subgroup and the headache-attack-period without aura sub group. Conclusions: COX-2 and visfatin participated in the pathogenesis of migraine headaches. The presence of aura had no effect on the serum levels of COX-2 and visfatin.