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The case-control association study design has been extensively used for elucidating the genetic basis of complex traits. Considerable variation in frequencies of various gene polymorphisms has been reported across different populations and ethnic groups. Thus before beginning such studies, one must know the gene variants that exist in the population. Such information is not available for the ethnically distinct Indian population, which, on the basis of the languages spoken, can be further subdivided into Indo-Europeans (North Indians) and Dravidians (South Indians). In this study we provide information on allele and genotype frequencies, pairwise linkage disequilibrium, and predominant haplotypes in two populations (North India, n = 96; South India, n =96) for several of the commonly investigated polymorphisms in the oxidative stress pathway genes. Of the 33 polymorphisms in 19 genes tested, significant differences in allele and genotype frequencies between the two populations were observed for SOD3 Ala58Thr, UCP1−3826 C/T, NOS3 −786 T/C, and TNFA −308 G/A polymorphisms.