Prolonged intake of aristolochic acid (AA) has been shown to be associated with the development of certain renal disorders. Renal tubular atrophy and interstitial fibrosis are the early symptoms of AA nephropathy. The symptoms were observed in rats that were dosed with AA at a dosage of 10 mg/kg/day for 1 month. Apart from the renal tubular atrophy and interstitial fibrosis, AA-DNA adducts were detected in the rat kidney tissue. Differentiated proteins were identified in the kidney tissues from proteomics investigations. The upregulated proteins identified included ornithine aminotransferase, sorbitol dehydrogenase, actin, aspartoacylase, 3-hydroxyisobutyrate dehydrogenase, and peroxiredoxin-1. Downregulated proteins such as ATP synthase subunit β, glutamate dehydrogenase 1, regucalcin, glutamate-cysteine ligase regulatory subunit, dihydropteridine reductase, hydroxyacyl-coenzyme A dehydrogenase, voltage-dependent anion-selective channel protein 1, prohibitin, and adenylate kinase isoenzyme 4 were also identified. Several identified protein markers were found to have biological and medical significance.