Understanding the possible impact of potential confounding factors is necessary for any approach to radiation biodosimetry. Potential confounding factors have not been fully addressed for gene expression-based biodosimetry approaches such as we are developing. To begin addressing this need we have used an ex vivo irradiated peripheral blood cell model to investigate the potential effect of smoking on the global radiation gene expression response and looked for genes that respond to radiation differently in smokers and non-smokers and also in males and females. The results indicate that only a small number of genes may be significantly confounded by either factor supporting the idea of developing peripheral blood gene expression strategies for radiation biodosimetry. Blood from each of 24 different donors was exposed to four doses of ionizing radiation (0 0.1 0.5 or 2 Gy) and analyzed using single-color microarray hybridization. The donors represented equal numbers of male and female smokers (1 or more packs a day) and non-smokers. There are 95 data sets in the study as the sample from one of the female smokers exposed to 2 Gy was lost.