NAD(P)H oxidase is one of the most important sources of reactive oxygen species and has been demonstrated to be upregulated by angiotensin II in the kidney. Given the effect of angiotensin-converting enzyme inhibitors on the progression of both diabetic and non-diabetic renal disease, we hypothesized that the polymorphisms of NAD(P)H oxidase are associated with development of end-stage renal disease (ESRD). We examined five polymorphisms in the CYBA gene encoding the p22 phox component of NAD(P)H oxidase, including 242C/T and 640A/G polymorphisms in 467 ESRD patients and 490 healthy individuals. The T allele of the 242C/T polymorphism showed a protective effect against ESRD only in the nondiabetic (non-DM) group (P = 0.0095), and haplotype estimation revealed that the frequency of 242C-640A was higher in the non-DM group (46.7%) than in the control group (39.7%). The CC-AA genotype was still significantly associated with ESRD without diabetes after adjusting for confounding factors (P = 0.035). In contrast, there was no difference between the DM group and the control group. In conclusion, we identified a risk haplotype for nondiabetic ESRD in the CYBA gene using haplotype analysis. Haplotype analysis proved useful for elucidating the genetic contribution of NAD(P)H oxidase p22 phox to ESRD.