2,4-dichlorophenoxyacetic acid (2,4-D) and nitrate are agricultural contaminants found in rural ground water. It is not known whether levels found in groundwater pose a human or environmental health risk, nor is the mechanism of toxicity at the molecular/cellular level understood. This study focused on determining whether 2,4-D or nitrate at environmentally realistic levels elicit gene expression changes in exposed cells. cDNA microarray technology was used to determine the impact of 2,4-D and nitrate in an in vitro model of exposure. Human hepatoma HepG2 cells were incubated with 2,4-D or nitrate alone for 24 h. Cell viability (neutral red assay) and proliferation (BrdU incorporation) were assessed following exposure. Total RNA from treated and control cells were isolated, reverse transcribed and reciprocal labelled with Cy3 or Cy5 dyes, and hybridized to a human cDNA microarray. The hybridized microarray chips were scanned, quantified and analyzed to identify genes affected by 2,4-D or nitrate exposure based on a two-fold increase or decrease in gene expression and reproducibility (affected in three or more treatments). Following filtering, normalization and hierarchical clustering initial data indicate that numerous genes were found to be commonly expressed in at least three or more treatments of 2,4-D or nitrate tested. The affected genes indicate that HepG2 cells respond to environmental, low-level exposure and produce a cellular response that is associated with alterations in the expression of many genes. The affected genes were characterized as stress response, cell cycle control, immunological and DNA repair genes. These findings serve to highlight new pathway(s) in which to further probe the effects of environmental levels of 2,4-D and nitrate.