Introduction: Anaemia is a blood disorder affecting about one fourth of the world’s population, particularly in pregnant women due to the high iron requirement. Among all types of anaemia, iron deficiency anaemia (IDA) is the most common. Recently, several genome studies identified many single nucleotide polymorphisms that influence blood cell phenotypes and participate in the causing anaemia. Particularly, TMPRSS6 (Trans–membrane protease, serine 6) gene SNPS rs 855791 polymorphism has a strongest association with red blood cell indices in general population. Methods: This study was conducted in 80 pregnant women with IDA and 80 healthy pregnant women without anaemia and investigated blood cell indices and TMPRSS6 rs855791 genotypes. Results: There were significantly fewer rs855791 C homozyogotes in the IDA group than in the healthy group (8.75% vs 26.25%, p=0.00362). The odds ratio (OR) of C homozygotes in IDA vs CT+TT genotypes in IDA was 3.71. Conclusion: Present study showed that TMPRSS6 gene SNP rs855791 CC genotype is less frequent in pregnant women with iron deficiency anaemia than in healthy mothers. This study recommends C homozogocity genotype for TMPRSS6 rs899791 has a protective role against IDA in pregnant women.