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Purpose: This study aimed at exploring MRI and 3D-TOF MRA in differential diagnosis of intra-arterial thrombosis and cervical artery dissection (internal carotid artery and vertebral artery) in different periods of disease using the contrast index. Methods and Materials: A total of 40 patients with extracranial artery dissection manifested by ischaemic stroke or isolated headache (20 men, 20 woman, mean age 37,3±6,1 years) and 8 patients (5 men, 3 woman, mean age 52,4±8,8) with ischaemic stroke due to intra arterial thrombosis were studied. Scanning protocol included 3D-TOF MRA sequence for extracranial internal and vertebral arteries and T1 fat suppression (f/s) sequence for neck in axial plane. MRT/MRA were carried in dynamics and obtained data were analysed in 6 time intervals: 1-3 days, 4-7 days, 8-14 days, 15-21 days, 22-60 days and 61-90 days. Intramural haematoma (IMH), intra artery thrombus (IAT) and m. sternocleidomastoid signal intensity was measured and contrast index calculated. Results: After statistical analysis of the data with the use of non-parametric statistical methods (Mann-Whitney U test) it was revealed that value of the contrast index of IMH was higher than that of IAT within 2-5 time interval (4 to 61 days) (p<0,05). The contrast index did not differ significantly within first 3 days and during 3 months. The subjective visual analysis showed the same results. Conclusion: MRI sequences as T1 f/s and 3D-TOF MRA could be useful for differential diagnosis of IMH and IAT within the interval of 4 days to 2 months of the disease.