Background: Iron deficiency anemia (IDA) is a global health problem and common medical condition seen in everyday clinical practice. Hepcidin which is the key regulator of iron homeostasis, that down-regulates iron export by binding to ferroportin which is expressed on the surface of iron-releasing cells, leading to its degradation thus reducing plasma iron levels. Overexpression of hepcidin leads to iron deficiency anemia. Matriptase-2 (MT-2) which is encoded by transmembrane protease serine 6 (TMPRSS6) gene regulates hepcidin expression. Objective: Was to evaluate the role of TMPRSS6 gene polymorphisms and serum hepcidin level in IDA patients. Subjects and methods: This study was carried out on 30 patients with iron deficiency anemia and 30 age and sex matched individuals as control group. Patients were subdivided into (group 1) 14 patients with acquired iron deficiency anemia (IDA) and (group 2)16 patients with iron refractory iron deficiency anemia(IRIDA).TMPRSS6 gene single nucleotide polymorphisms(SNPS), (rs4820268)and(rs855791)were evaluated using real time – polymerase chain reaction (RT-PCR) while serum hepcidin level was measured by enzyme linked immunosorbent assay (ELISA). Results: There was a significant increase in frequency of the TMPRSS6 SNPs rs855791 and rs 4820268 separately in IRIDA group compared to IDA group,(P=0.003),(P=0.007) respectivelyand to control group(P=0.000) and (P=0.000) respectively.Also, there was highly significant increase in frequency of both mutations together in IRIDA group compared to IDA group (P=0.000) and to control group (P=0.000). In IDA group there was a significant increase in the frequency of TMPRSS6 SNPs rs 855791 when compared to control group (P=0.013), and a non-significant difference in frequency of SNPs rs 4820268 when compared to control group (P=0.092).Also, there was a non-significant difference in frequency of both mutations together in IDA group in comparison to control group (P> 0.05).There was a highly significant decrease in serum hepcidin level in IDA group and  highly significant increase in hepcidin levels in IRIDA group compared to control group (P=0.000).In IRIDA patients group only there was highly significant increase in hepcidin level in those with mutation in both SNPs together  (rs4820268 and rs855791) than patients with one mutation or with wild type(P=0.000).There was a significant decrease in Hb and iron and highly significant decrease in MCV, MCH and ferritin  in IRIDA patients with mutation of both SNPs together (rs 4820268 and rs855791) compared to one mutation or wild type (P=0.015,0.016,0.002 ,0.000, 0.006 respectively).Also, there was highly significant decrease in Hb, MCV, MCH and ferritin in IDA patients with mutation of both SNPs together(rs 4820268 and rs 855791) compared to one mutation or wild type (P= 0.002,0.002 ,0.004, 0.009 respectively). In IDA patients there was a significant positive correlation between hepcidin and ferritin (P =0.034, r = 0.279),while there was a significant negative correlation between hepcidin and MCH in IRIDA group (P =0.032, r = - 0.536).Conclusion: In IRIDA the rs4820268 and rs855791 mutations separately or in combination lack inhibitory effect on hepcidin and consequently iron profile and hemoglobin while in IDA although there was significant increase in frequency of rs855791 mutations, there was no effect on hepcidin which suggests that the rs 4820268 mutation is necessary for affecting hepcidin either alone or in combination with rs 855791 mutation. In IDA, there may be other mechanisms or mutations causing anemia.