Spinal cord injury (SCI) is a devastating condition with important functional and psychological consequences. However, the underlying mechanisms by which these alterations occur are still not fully understood. The aim of this study was to analyze genomic instability in multiple organs in the acute phase of SCI by means of single cell gel (comet) assay. Rats were randomly distributed into two groups (n = 5): a SHAM and a SCI group killed 24 h after cord transection surgery. The results pointed out genetic damage in blood cells as depicted by the tail moment results. DNA breakage was also detected in liver and kidney cells after SCI. Taken together, our results suggest that SCI induces genomic damage in multiple organs of Wistar rats.