Spinal cord injury (SCI) produces multiple systemic and metabolic alterations. Although some systemic alterations could be associated with ischemic organ damage, little is known about microvascular blood flow (MVBF) in organs other than the spinal cord after acute SCI. We used laser Doppler flowmetry in anesthetized rats to assess MVBF in several tissues before and after complete T-2 and T-9 SCI at 1 h and on days 1, 3, and 7 post-SCI. Mean arterial blood pressure (MAP), heart rate and hematologic variables also were recorded. MAP changes after T-2 injury were not significant, while MAP decreased significantly 1 h after T-9 injury. Statistically significant bradycardia occurred after T-2 injury at 7 days; statistically significant tachycardia occurred after T-9 injury at 1, 3, and 7 days. Hematocrit significantly increased at day 1 and decreased at days 3 and 7 after T-2 injury. SCI was associated with significant decreases in MVBF in liver, spleen, muscle and fore footpad skin. Changes in MVBF in hind footpad skin and kidney were not significant. Changes were more pronounced at 1 h and 1 day post-SCI. Significant differences between MVBF after T-2 and T-9 SCI occurred only in liver. MVBF significantly correlated with regional peripheral vascular resistances (assessed using the MAP/MVBF ratio), but not with MAP. In conclusion, organ-specific changes in systemic MVBF that are influenced by the level of SCI, could contribute to organ dysfunction.