Gene expression profiling is considered as a promising tool that may identify more sensitive, mechanism-based biomarkers. Such an experimental approach should provide a better understanding of the impact of chemical compounds on the intracellular mechanisms leading to different pathologies. The purpose of this study was to evaluate and to compare the impact of mainstream cigarette smoke from two commercial blends, on the modulation of gene expression in A549 cells, a type II alveolar epithelial human cell line. Cells were exposed to cigarette smoke at various concentration levels for 20 h. After treatment, RNA was extracted, cDNA synthesized and gene expression analyzed on a cDNA macroarray spotted with 288 toxicologically relevant genes (Human Oligo GEArray→, membrane EHS 401). Global gene expression analysis was conducted in three steps using R-Statistical computing. Initially, a normalization based on the "quantile method" was used to produce comparable arrays. In a second step, a discriminate analysis was performed to select the most relevant genes for differentiating the effect of smoke from the respective cigarettes. A third step consisted in confirming the significant differences in gene expression with two statistical analysis : SAM and PAM (Significant and Predictive Analysis Methods). Cigarette smoke significantly modulated the expression of some genes. As an example, the genes allocated to the weakest TPM-concentration are either associated with cell cycle regulation or transcription factors: TP53, PCNA, and SAFB. Discrimination between blends was observed with those genes. In the higher TPM-concentration, no genes involved in DNA damage were modulated; however, some genes involved in metabolism such as GAL3ST1, GPX1, and PON3 were modified. In conclusion, several genes were identified as potential biomarkers of early biological effects caused by mainstream cigarette smoke exposure in our in vitro experimental conditions.