Vascular sclerosis is often seen in renal biopsies. It is usually associated with diabetes mellitus, hypertension, smoking, etc. However, whether inherited thrombophilic states such as factor V gene mutation, prothrombin gene mutation, and methylenetetrahydrofolate reductase (MTHFR) gene mutation are associated with the vascular sclerosis is not known. Renal biopsies that showed vascular disease were grouped into five groups: (1) diabetic patients, (2) hypertensive patients, (3) diabetic and hypertensive patients, (4) smokers, and (5) vascular sclerosis of unknown etiology (idiopathic renal disease). Renal biopsies with no vascular sclerosis were used as controls. Frozen tissue was analyzed for factor V Leiden mutation, prothrombin G20210A mutation, and MTHFR C677T. Factor V Leiden mutation and prothrombin G20210A mutation was not seen in patients with diabetes, hypertension, or smoking, whereas MTHFR C677T polymorphism in these groups was not significant, compared to the controls. In the idiopathic renal disease group, three of the 17 patients (17.6%) had prothrombin G20210A mutation, two of the 17 patients (11.8%) had the factor V Leiden mutation, and five of the 17 (29.4%) were homozygous for the MTHFR C677T polymorphism. When the data were evaluated as a whole, 10 mutations were found in 17 patients (P<0.0005 compared to controls) or eight of the 17 patients (47%) were observed to have at least one of the three forms of inherited thrombophilia (P<0.001 compared to controls). These findings indicate that renal vascular lesions, in the absence of diabetes, hypertension, or smoking appears to be associated with inherited thrombophilias.