We recently reported mutation analysis of the largest cohort of Glanzmann thrombasthenia (GT) patients so far examined. Sanger sequencing of coding regions, splice sites, upstream and downstream regions of the ITGA2B and ITGB3 genes identified 78 causal genetic variants (55 novel); 4 large deletions or duplications were also detected. We have now analysed the expression of non-causal gene polymorphisms in the sequenced regions of both genes in selected members of this cohort. We identified 10 mostly silent variants in ITGA2B and 37 in ITGB3; all were present in control donor databases. Three non-synonymous single nucleotide polymorphisms present were human platelet alloantigen (HPA) variants. A series of haplogroups, often including HPA-3b in ITGA2B, repeated with little variation across unrelated families of wide geographical origins and with different GT-causing mutations whether in ITGA2B or ITGB3. In contrast, a deleterious heterozygous c.1440-13_c.1440-1del in intron 14 of ITGA2B shared a common ITGA2B haplogroup composed of at least five gene polymorphisms and re-occurred in seven European families with no known family relationships. Our results highlight the value of gene polymorphism analysis in GT and are consistent with the bulk of disease-causing mutations in GT being of recent origin.