In this study, we showed, using comprehensive gene expression analysis, that pertussis and pandemic influenza vaccine affected many lung genes. The 13 and 76 genes were extracted from the pertussis vaccine- and pandemic influenza vaccine-treated lung at day 1, respectively. Furthermore, QuantiGene Plex methods, quantitative analysis of the expression of these genes could detect the toxicity from samples containing various concentrations of reference pertussis vaccines. Our findings and methods provide the first assessment for the influence of vaccine toxicity with an approach using experimental biology and genome science.