Polymorphism of clotting factor V, comprising Arg506Gln substitution in the factor V molecule, commonly known as Factor V Leiden, represents the most common heritable risk factor for thrombotic events in Indo-Europeans and some Semitic nations. Although it is suggested that this mutation is associated with a survival advantage that has facilitated the spread of this polymorphism in the human population, in this paper we argue against such a Darwinian evolutionary mechanism responsible for the high prevalence of FV Leiden in some countries. Instead, we propose that cultural, climatic, and geographic factors played a role. Taking into account the current distribution of FV Leiden polymorphism and the results of recent assessments of prehistoric human DNA, we suggest that actually the origin of FV Leiden mutation did not occur in the Near East, as is widely believed, but rather in a small isolated population of so-called Basal Eurasians, probably in northern Africa. This founder group probably migrated to the Near East during the Younger Dryas, a geological period associated with climate cooling. Here, they mixed with local people; still Factor V Leiden mutation remained very prevalent in this population. The invention of agriculture, which took place approximately 2,000 years later, gave the descendants of Basal Eurasians an enormous advantage over hunter-gatherers, and probably enabled a successful spread of FV Leiden polymorphism to Europe, Central Asia, and towards the Indian subcontinent.