Oxidative stress is implicated in disease and aging. In order to obtain molecular genetic tools that can be used to determine the potential impact of oxidative stress we examined the human catalase gene promoter for possible variation. Genomic DNA isolated from 10 individuals was screened for polymorphisms in the 5'-flanking region by direct sequence analysis of PCR products (nt -307 to -46 from the transcription start site). A common C/T polymorphism -262 base pairs from the transcription start site was detected. Computer analysis indicated that the two variants bound different transcription factors. Indeed, gel retardation analysis revealed different protein binding patterns to the two variants. Expression studies with reporter constructs showed significantly higher transcriptional activity of the T variant in HepG2 and K562 cells (1.5-fold,p <.05 Wilcoxon test). Thus a higher expression in human liver and blood cells is possible. In order to test this hypothesis, catalase levels in red blood cells were determined in 29 donors. The corresponding genotype was determined with a restriction enzyme-based assay. It was found that catalase levels were significantly higher in donors carrying the T allele in comparison to donors homozygous for the C allele (p <.03). In conclusion, we report here the first common (allele frequency in a Swedish population, 28%) genetic variant in a fundamental oxidative stress protection gene with a defined phenotype.