Objectives: Throughout evolution high degree of polymorphism of human leukocyte antigens (HLA) has been observed which ensured accommodation and presentation of all possible antigens. Non-classical human leukocyte antigens-G (HLA-G) region shows polymorphism at 5′-upstream regulatory region (5′-URR) and in the 3′-untranslated region (3′-UTR). These polymorphisms have not been explored extensively in spite of the fact that they have been associated with immune-modulation. This study explores the HLA-G allele diversity and their plausible role in reshaping the global population structure. Methods: Three hundred North Indians were screened using HLA-G 5´URR region by sequencing. The 14 bp insertion deletion polymorphism was evaluated by polymerase chain reaction (PCR) followed by polyacrilymide gel electrophoresis (PAGE). Detailed statistical analysis was done to compare the present population with allele frequency data of 12 global populations. The number of populations was restricted as only sequence based typing based studies were considered. Results: The genetic distance, phylogenetic analysis and principal component analysis revealed genetic similarity of North Indians with populations of West Eurasian descent from HLA-G allelic diversity view point. Mongoloid, African, and South American populations revealed less genetic similarity with North Indians. Conclusions: Indian subcontinent has undergone many historical migrations and invasions hence it is intriguing to observe how the conserved HLA-G has behaved from the population diversity view point throughout these years. Our results revealed less genetic distance with Caucasians suggesting an evolutionary link among them.