Hyperoxaluria associated with renal deposition of calcium oxalate (CaOx) crystals causes renal injury and inflammation leading to number of diseases including chronic kidney disease (CKD). It is however, not been possible to separate the renal consequences of hyperoxaluria from that of CaOx crystal deposition. We decided to utilize ethylene glycol (EG) model where hyperoxaluria and CaOx crystal deposition can be separated in time. To test our hypothesis, male rats were made hyperoxaluric by administering EG, rats were euthanized and kidneys were extracted on day 14, when occasional crystal is seen in the kidneys and day 28, when all animals have developed renal CaOx crystal deposits. Total RNA was extracted for microarray analysis and genome wide analysis of differentially expressed genes was performed to investigate differences between hyperoxaluria and crystal induced alterations in the kidneys. Immunohistochemical and Hematoxylin and Eosin (H&E) staining was also done for macromolecules with significant role in stone formation. All EG fed rats became hyperoxaluric by day 7, showed a few crystal deposits on day 14, and had heavy crystal deposition by day 28. There were significant changes in the expression of genes encoding for NADPH Oxidases; macromolecular crystallization modulators; genes involved in inflammasome activation; and osteogenic marker genes. Results demonstrate major differences between hyperoxaluria and CaOx crystal induced changes in the kidneys. Injury and inflammation are mainly associated with crystal deposition indicating significant role played by crystal retention.