Cigarette smoke from conventional tobacco products contains more than 5300 identified constituents, some of which are associated with smoking-related diseases in smokers. While there is considerable knowledge about the direct toxicity of cigarette smoke and some of its constituents at high test concentrations, far less is known about the subtle mechanistic effects of cigarette smoke and the individual constituents that may induce disease at biologically relevant concentrations in target tissues. A tiered approach to assess these mechanistic effects using in vitro-based assays was developed. Initially, the toxicological and pathophysiological profiles of single cigarette smoke constituents will be determined in viability, proliferation, and apoptosis assays. In subsequent tiers, a step-wise reduction of test compound numbers according to set criteria and assay outcomes will lead to more complex, mechanism-based assays for pathophysiological assessments. The immediate target of inhaled cigarette smoke is the lung; therefore, cultured primary human bronchial epithelial cells will be used for the initial assays. Compounds not active in viability, proliferation, or apoptosis assays may have specific modes of action that lead to adverse physiological effects (pathophysiology) in an intact organism. Examples are genotoxic compounds that either do not affect normal cell function in the short term (e.g., polycyclic aromatic hydrocarbons [PAH]) or have a non-genotoxic tumor-promoter-like activity or interference with receptor functions (e.g., estrogen receptors). Thus, assays are selected for assessing target-specific effects of single compounds. In the following tiers, systems biology approaches will be used to generate high density data (mRNA arrays, reverse proteomics arrays, gene copy number arrays) for correlation to functional data obtained at biologically relevant experimental conditions. This will enable the identification of new responsive genes, their implication in cellular pathways, and the understanding of compound-affected network perturbations in biological processes that lead to smoking-related diseases.