We examined the effect of eccentric exercise on the transcriptome of skeletal muscle in three male human volunteers who performed 300 concentric contractions with one leg and 300 eccentric contractions with the opposite leg. Vastus lateralis muscle biopsies were taken from both legs at 4-8 h after exercise, and expression was profiled by using 12000 gene Affymetrix U95Av2 microarrays. We found a high concordance of expression responses to eccentric contractions between our human and rat data from a previous study (Chen YW, Nader GA, Baar KR, Fedele MJ, Hoffman EP, and Esser KA. J Physiol 545: 27-41, 2002) ( approximately 50% of gene expression changes shared between species). Potential human-specific changes included greater inflammatory responses [chemokine (C-C motif) ligand 2, C/EBP delta, and IL-1 receptor] and vascular remodeling (tenascin C and lipocortin II). Induction of c-fos and lipocortin II were confirmed at the protein level, with c-fos localized to myofiber nuclei and lipocortin II to intramuscular capillaries. We also confirmed the eccentric-induced expression of six transcripts by quantitative RT-PCR (cardiac ankyrin-repeated protein, chemokine ligand 2, CCAAT/enhancer binding protein delta, IL-1 receptor, tenascin C, and cysteine-rich angiogenic inducer 61). These data provide the first characterization of the transcriptional response of skeletal muscle to eccentric exercise in humans and represent a preliminary step in understanding the molecular processes underlying muscle remodeling (including a new focus on rapid changes in the capillary bed) and inflammatory responses after damaging lengthening contractions.