Many mechanisms of neurodegeneration have been implicated in Parkinson's disease, but which ones are most important and potential interactions among them are unclear. To provide a broader perspective on the parkinsonian neurodegenerative process, we have performed a global analysis of gene expression changes caused by chronic, low-level exposure of neuroblastoma cells to the mitochondrial complex I inhibitor and parkinsonian neurotoxin rotenone. Undifferentiated SK-N-MC human neuroblastoma cells were grown in the presence of rotenone (5 nM), and RNA was extracted at three different time points (baseline, 1 week, and 4 weeks) for labeling and hybridization to Affymetrix Human U133 Plus 2.0 GeneChips. Our results show that rotenone induces concerted alterations in gene expression that change over time. Particularly, alterations in transcripts related to DNA damage, energy metabolism, and protein metabolism are prominent during chronic complex I inhibition. These data suggest that early augmentation of capacity for energy production in response to mitochondrial inhibition might be deleterious to cellular function and survival. These experiments provide the first transcriptional analysis of a rotenone model of Parkinson's disease and insight into which mechanisms of neurodegeneration may be targeted for therapeutic intervention.