GeneChip microarrays have recently been introduced to the field of neurobiology to identify and monitor the expression levels of thousands of genes simultaneously. This powerful technique is now used for studying the pathophysiology of CNS injuries including spinal cord lesions. Early stages after injury are characterized by the strong upregulation of genes involved in transcription and inflammation and a general downregulation of structural proteins and proteins involved in neurotransmission. Later, an increase in the expression of growth factors, axonal guidance factors, extracellular matrix molecules and angiogenic factors reflects the attempts for repair, while upregulation of stress genes and proteases and downregulation of cytoskeletal and synaptic mRNA reflect the struggle of the tissue to survive. DNA microarrays have the potential to aid discovery of new targets for neuroprotective or restorative therapeutic approaches