Smoking causes serious fatal diseases such as lung cancer and chronic obstructive pulmonary disease. Bronchial epithelial cells as the first barrier against invading organisms and exposure to chemicals play a major role in the pathogenesis of these diseases. In order to demonstrate the applicability of a Systems Toxicology Approach to evaluate the risk associated with prototypic Modified Risk Tobacco Products (pMRTPs), normal Human Bronchial Epithelial (nHBE) cells were exposed to an aqueous cigarette smoke fraction (smoke bubbled into phosphate-buffered saline/sbPBS) from the 3R4F reference cigarette at three non-toxic doses based on cell viability for either 4 or 24 hours. The pMRTP aerosol doses in sbPBS were matched to the highest concentrations of 3R4F in terms of puff/ml. A static headspace GC/MS method focusing on volatile and semi-volatile constituents revealed that most of the levels of the 85 monitored constituents were lower in sbPBS of the pMRTP as compared to the 3R4F. Whole genome transcriptomics analysis of nHBE cells demonstrated a dose-dependent increase in the number of differentially expressed genes for the 3R4F sbPBS exposure. Fewer genes were differentially expressed after exposure to sbPBS from the pMRTP. Analysis using computable biological network models showed the perturbation of biological processes related to cell stress and senescence after 4 hours of exposure to sbPBS from 3R4F, whereas after 24 hours of exposure the cell proliferation network was most perturbed. Exposure to the pMRTP resulted in much attenuated perturbation of biological networks. In summary, we provide mechanistic insight of the biological impact on key cellular processes in nHBE cells upon sbPBS exposure, suggesting reduced biological network perturbation from exposure to pMRTP compared to 3R4F.