Background: Cryptogenic stroke means stroke with unexplained aetiology in 1/3 of cases. The cause of stroke remains undetermined inspit of full investigations. Those patients are thought to have hypercoagulable stat. Purpose of study: is to unmask some of the pathogenic mechanisms underlying cryptogenic stroke through assessment of some generic disorders including C677T mutation in methylenetetrahydrofolate reductase gene and activated protein C (APC) resistance, and role of thrombin anti-thrombin complex concentration in plasma as indicator of hypercoagulable state. Subject and Methods: study was conducted on 10 Egyptian patients (4 females and 6 males) with cryptogenic stroke who are less than 50 years (group I) and 10 age and sex matched patient with non-cryptogenic stroke (group II). They were subjected tpanel of investigations including all routine labs and imaging studies in order to exclude any risk factors for stroke in group I patients and to determine risk factors of stroke in group II, then both groups are investigated for C677T mutation in methylenetetrahydrofolae reductase gene, activated protein c (APC) resistance, thrombin anti-thrombin complex concentration in plasma (P value > 0.05), TAT level was positively correlated with clinical severity in non-cryptogenic stroke (P vaue < 0.05). Conclusion : C677T mutation in methylenetetrahydrofolate reductase gene, activated protein C(APC) resistance, thrombin anti-thrombin complex concentration in plasma are notindependent risk factor for crtyptgenic stroke, TAT could be used as indicator of clinical severity and prognosis in patient with non-cryptogenic stroke.