BACKGROUND Epidemiological studies indicate that over the past forty years, the stroke incidence rates has increased. Factors V and II mutations are established genetic-variant risk factors for venous thrombosis; however, their contribution to stroke is a controversial issue. OBJECTIVES This study aimed to investigate the potential association of FV and FII mutations with stroke in an Iranian population. PATIENTS AND METHODS The study population consisted of 153 patients of different stroke subtypes (except cryptogenic strokes), admitted to Ghaem Hospital, Mashhad, Iran. The control group included 153 age- and sex-matched subjects without a history of cerebrovascular or neurologic diseases. Mutations of FV and FII were determined by using a TaqMan SNP Genotyping technique. The chi-square and Exact Fisher tests were used to analyze the baseline characteristics. Results were as follows: The calculated P-value for sex and diabetes mellitus were 0.907 and 1.000, respectively. The case and control groups were also matched in low density lipoprotein (P = 0.816), high density lipoprotein (P = 0.323), triglyceride (P = 0.846), and total cholesterol (P = 0.079). RESULTS Analysis of the FV showed that none of the study subjects were AA homozygous for this mutation and only 6 heterozygous subjects were detected in the case and control groups. Regarding FII variants, none of the study subjects were AG heterozygous and only 1 AA homozygous was detected in the control group. CONCLUSIONS The prevalence of both FV and FII variants are population based. Iran is an ethnically diverse country. Therefore, for a comprehensive analysis of a potential association of FV and/or FII mutations with stroke among Iranian population, epidemiological studies could be conducted among different ethnic groups.