Matrix metalloproteinases (MMP) are the enzymes responsible for proteolytic activity of extracellular matrix proteins. Tissue inhibitors of metalloproteinases (TIMPs) are their endogenous inhibitors. MMP-9 acts on the basal membrane of cerebellar epithelium and is antagonized by TIMP-1. MMP-9/TIMP-1 ratio exhibits the net activity of MMP-9. These enzymes are thought to have a role in migraine physiopathogenesis. Total of 50 treatment-naive migraine patients (25 with aura and 25 without aura) with no other diseases, were included. 25 healthy control subjects of corresponding age and gender were enrolled. For MMP-9 and TIMP-1 analysis, one serum sample from control group and two samples from patients were collected (during headache and headache-free periods). The enzyme levels were quantitatively analyzed by competitive ELISA method. Duration and severity of the pain and duration of the disease were recorded. There was no significant difference in MMP-9 levels between patient and control groups during headache and headache-free periods (p: 0,746, p: 0,243). TIMP-1 levels were significantly lower and MMP-9/TIMP ratios were higher comparing with the control group (p: 0.001). Positive correlation was obtained between the duration of pain and MMP-9 levels in the headache-free period for both patient groups (p<0.05). There was also a positive correlation between MMP-9/TIMP-1 ratio and severity of pain (p<0.05). In our study, low TIMP-1 levels of patients in both headache and headache-free periods suggest that disturbance of proteolytic protection has a role in neuro-inflammation and pain in migraine. Therefore, these enzymes could be potential targets in migraine therapies.