The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) induces cellular DNA damage and other comprehensive alterations that lead to chromosomal aberrations, mutations, tumor initiation, and cell death. However, the molecular mechanism of MNNG-induced cellular stress remains unclear. We undertook a genome-wide analysis of early transcriptional responses of human FL amnion epithelial cells to three relatively low doses of MNNG (0.2, 1.0, and 10.0 microM). Using Affymetrix GeneChip HG-U133 Set oligonucleotide microarrays, a total of 281 genes were found to change their expression after exposure to all three doses of MNNG compared with the vehicle control, DMSO. Of these, 70, 112, and 146 genes showed different expression levels following treatment with low, medium, and high-dose MNNG, respectively. A subset of these genes were selected for further confirmation using quantitative real-time RT-PCR with ABI TaqMan((R)) low-density arrays, and the differential expression of 33 genes was validated. The results demonstrate that low doses of MNNG can induce various changes in gene expression at an early stage of exposure. The responsive genes are involved in multiple cellular biological processes including transcription regulation, signal transduction, cell cycle regulation, cytoskeleton organization, protein synthesis, immune responses, and metabolism. The cell cycle progression was down-regulated, in which several genes were validated involved, including the cell cycle regulators (CDK6, STK6, CENPA, and CCNF), the transcription factor ID-1, and the calcium signaling molecules (CAMK2G and NFAT5). The possible roles of the responsive genes and their related pathways in MNNG-induced cellular responses are discussed. This study helps to complete the picture of how cells respond to environmental chemical exposure via transcriptional regulation.