Functional and structural abnormalities in the renal microvasculature are important processes contributing to the pathophysiology of ischemic acute kidney injury (AKI). In this study we examine the contribution of endothelial cell loss via apoptosis on microvascular permeability and rarefaction in a mouse model of ischemic AKI. Three-dimensional reconstructions of microvascular networks obtained 24 hours following acute ischemic injury demonstrate an intact endothelial monolayer in areas of increased microvascular permeability. A 45% decrease in microvascular density was observed four weeks after acute ischemic injury. Examination of microvascular endothelial cells following acute ischemic injury did not reveal evidence of positive TUNEL staining at 1, 2, 8, and 16 days following ischemia; however, activation of caspase-3 was evident in endothelial cells following acute ischemic injury. Examination of angiopoietin protein expression in the kidney twenty-four hours after ischemic injury revealed an 8 fold increase in angiopoietin-1 (ang-1) but no significant change in angiopoietin-2 (ang-2). No significant difference in the expression of vascular endothelial growth factor (VEGF) or ang-2 was observed four weeks after ischemic injury although an almost two-fold elevation in ang-1 was observed. An increase in angiostatic breakdown products of collagen IV was observed at both 24 hours and 4 weeks after ischemic injury. Taken together these findings indicate that the loss of endothelial cells following ischemic injury is not a major contributor to altered microvascular permeability although renal microvascular endothelial cells are vulnerable to the initiation of apoptotic mechanisms following ischemic injury that can ultimately impact microvascular density.