NQO1 NAD(P) kinon has a protective effect against benzen toxicity due to its detoxifying activity. It has been suggested that individuals with NQO1 deficiency are more susceptible to benzen toxicity.The aim of the present research is to determine NQO1 genetic polymorphism in patients with primary (pMDS) and secondary myelodisplastic syndrome (sMDS) and to search the relation between polymorphisms and cytogenetic abnormalities. Clonal chromosomal abnormalites were found in 53.75 % of patients with MDS in our studies. The most frequent cytogenetic aberrations were complex anomalies (%18.75) , -7/del(7q)(%10) , -5/del(5q) /der(5q)(%8.75) , +mar (%6.25), +21(%.5), -17(%5)-14(%5), +8 (%3.75), t(8;21)(q22;q22) (%3.75), -8(%3.75), -21(%3.75) and +22(%3.75). The NQO1 gene was analysed with respect to the presence of C609T mutation by using PCR-RFLP. Patients with MDS are classified in the 4 subgroups: 1-Patients with hypocellular bone marrow (OR: 0,625 , %95 CI: 0,334-1,169, p=0,138 ) 2-Patients with hypercellular bone marrow (OR:1,448, %95 CI :0,689-3,045, p=0,326) 3-Patients with pediatric MDS (OR,0,721,%95 CI , 0,267-1,947,p=0,517). 4- Patients with sMDS (OR,1,893,%95 CI,0,840-4,265,p=0,118). In our study, C609 T allelic frequency was not different than the controls (OR,0,891,%95 CI , 0,22-1,518,p=0,670). In addition, some patients with cytogenetic abnormalities are frequently seen in all subgroups, so we classified them as a seperate group. We found that the C609T allele was and 3.038 times more frequent in patients with the t(8;21) anomaly (OR,3,084,&95 CI , 0,604-15,172 , p=0,170) compared to the controls. However, none of these results were statistically significant.