In this study we aimed to identify genes that are responsive to pertussis toxin (PTx) and might eventually be used as biological markers in a testing strategy to detect residual PTx in vaccines. By microarray analysis we screened six human cell types (bronchial epithelial cell line BEAS-2B, fetal lung fibroblast cell line MRC-5, primary cardiac microvascular endothelial cells, primary pulmonary artery smooth muscle cells, hybrid cell line EA.Hy926 of umbilical vein endothelial cells and epithelial cell line A549 and immature monocyte-derived dendritic cells) for differential gene expression induced by PTx. Immature monocyte-derived dendritic cells (iMoDCs) were the only cells in which PTx induced significant differential expression of genes. Results were confirmed using different donors and further extended by showing specificity for PTx in comparison to Escherichia coli lipopolysaccharide (LPS) and Bordetella pertussis lipo-oligosaccharide (LOS). Statistical analysis indicated 6 genes, namely IFNG, IL2, XCL1, CD69, CSF2 and CXCL10, as significantly upregulated by PTx which was also demonstrated at the protein level for genes encoding secreted proteins. IL-2 and IFN-γ gave the strongest response. The minimal PTx concentrations that induced production of IL-2 and IFN-γ in iMoDCs were 12.5 and 25IU/ml, respectively. High concentrations of LPS slightly induced IFN-γ but not IL-2, while LOS and detoxified pertussis toxin did not induce production of either cytokine. In conclusion, using microarray analysis we evaluated six human cell lines/types for their responsiveness to PTx and found 6 PTx-responsive genes in iMoDCs of which IL2 is the most promising candidate to be used as a biomarker for the detection of residual PTx.