Headaches are one of the most common ailments in modern society, leading to severe diminishing of patients’ general and work activities during an attack and resulting in a significant impact on the quality of life, as well as causing substantial economic costs for their treatment. Despite numerous research projects on the pathophysiology of specific types of headaches, it still remains insufficiently understood. Blink reflex is an objective neurophysiologic method for determining the status of the trigeminal system, facial nerve and the lateral part of medulla oblongata. Blink reflex tests on patients suffering from migraines and control group consisting of persons not suffering from migraines have shown dubious results. The objective of the research is to try and prove the correlation between trigeminal nerve dysfunction and its causes in various types of headaches by applying functional electrophysiological and radiological methods of display, and to analyse trigeminal nerve functions using blink reflex tests in patients suffering from headaches. The presence of trigeminal nerve dysfunction would point to another potential path for targeted therapies in patients suffering from headaches, resulting in improvements in their quality of life. It is our hypothesis that it is possible to determine trigeminal nerve dysfunction by analysing the blink reflex in patients suffering from headaches. Subjects and methods: The main group consists of subjects in which the occurrence of headache attacks has been determined by a survey. The control group consists of subjects who are free from headaches, but experience pain in cervical and lumbar spine. The main and control groups have been age adjusted. Results: The research clearly shows that pathological findings of blink reflex are found in 58.3 % of patients suffering from headaches and in only 20 % of cases in the control group of headache-free patients. The application of Yates Correction χ2 indicates a significant correlation between the pathological blink reflex and headache occurrence (χ2 = 10.354; P = 0.001). Normal blink reflex was found in 41.7 % of patients suffering from headaches and in 80 % of control group subjects. The calculation of the relative risk of headaches shows that subjects with a pathological blink reflex have 5.6 times higher risk of developing headaches than persons with a normal blink reflex. Headaches occur quite often in persons with a pathological blink reflex (in 58 % of cases), while normal blink reflex findings occur in 80 % of cases in the control group. The research shows that conclusions reached on the basis of statistical tests coincide regardless of sex. Conclusion: There is a strong correlation between the pathological blink reflex and the occurrence of headaches, regardless of age and sex of patients, indicating statistically significant correlation between the occurrence of headaches and trigeminal nerve dysfunction.