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Background Spinal cord injury (SCI) is a complex trauma that consists of multiple pathological mechanisms involving cytotoxic, oxidation stress and immune-endocrine. This study aimed to establish plasma metabonomics fingerprinting atlas for SCI using 1H nuclear magnetic resonance (NMR) based metabonomics methodology and principal component analysis techniques.Methods Nine Sprague-Dawley (SD) male rats were randomly divided into SCI, normal and sham-operation control groups. Plasma samples were collected for 1H NMR spectroscopy 3 days after operation. The NMR data were analyzed using principal component analysis technique with Matlab software.Results Metabonomics analysis was able to distinguish the three groups (SCI, normal control, sham-operation). The fingerprinting atlas indicated that, compared with those without SCI, the SCI group demonstrated the following characteristics with regard to second principal component: it is made up of fatty acids, myc-inositol, arginine, very low-density lipoprotein (VLDL), low-density lipoprotein (LDL), triglyceride (TG), glucose, and 3-methyl-histamine.Conclusions The data indicated that SCI results in several significant changes in plasma metabolism early on and that a metabonomics approach based on 1H NMR spectroscopy can provide a metabolic profile comprising several metabolite classes and allow for relative quantification of such changes. The results also provided support for further development and application of metabonomics technologies for studying SCI and for the utilization of multivariate models for classifying the extent of trauma within an individual.