Background: We aimed to investigate the effect of angiotensin II inhibition on the expression of angiogenesis-related genes and microvascular endothelial cells in neonatal rat kidney. Methods: Newborn rat pups were treated with enalapril (30 mg/kg/d) or vehicle for 7 days after birth. The grade of tubular injury and glomerular maturity was determined by hematoxylin and eosin stain. Intrarenal expressions of angiopoietin-1, angiopoietin-2, Tie-2, and thrombospondin-1 were investigated with Western blots and immunohistochemical staining at postnatal day 8. For determination of capillary density, the endothelial cell marker aminopeptidase P (JG-12) was also assessed. Results: Enalapril-treated rats demonstrated a higher score of tubular injury and a lower grade of glomerular maturity (p<0.05). In the enalapril-treated group, angiopoietin-2, Tie-2 and thrombospondin-1 protein expression were significantly increased whereas angiopoietin-1 expression was decreased, as compared to the control group (p<0.05). Immunohistochemical staining of kidney sections for JG-12 showed a dense capillary network in cortex and medulla from control rats; however, enalapril-treated kidney showed a reduced endothelial immunostaining (p<0.05). The number of JG12-positive endothelial cells showed a positive correlation with the grade of glomerular maturation (r=0.948, p<0.001) and a negative correlation with the tubular alteration grade (r= -0.842, p<0.05). Conclusion: Our findings suggest that enalapril treatment can induce the dysregulation of angiopoietin system and thrombospondin-1 genes and the loss of renal microvasculature, which may be relevant to the pathogenesis of structural deterioration caused by angiotensin II inhibition in the neonatal rat kidney.