Objective. To study the informative nature of manual therapy for differential diagnosis of migraine and cervicogenic headache (CH). Material and methods. The authors analyze two clinical cases of patients with a previously established diagnosis of migraine, with the duration of the disease of over ten years and neuroimaging signs of degenerative-dystrophic changes in the upper cervical spine. In both cases, there was no hereditary history and low efficacy of the previous drug therapy was noted. The informative value of the tests performed by methods of manual medicine followed by manipulation procedures of neck structures for the differential diagnosis of migraine and CH was assessed. Results. Despite the absence of complaints, both patients demonstrated the limitation of the volume of neck movements during the tests performed by methods of manual medicine. After a course of manipulation procedures, headaches in both patients were completely stopped for a period of six to ten months. The analysis of literature suggests that manipulative effects on neck structures in cases of migraine can reduce the intensity and the duration of pain, and the frequency of attacks by no more than 20%. The therapeutic effectiveness of manual therapy for CH is much higher; this method provides an opportunity to reduce the severity of these pain characteristics by 30—80%. These results are the basis for changing the previously established diagnosis to CH. Conclusion. The complex of diagnostic and therapeutic techniques of manual therapy is an important tool for the differential diagnosis of migraine and CH.