Introduction: This study was done to assess the injurious effects of omeprazole by an in vivo experimental study on rat kidneys. Materials and Methods: Forty-two adult male albino rats were divided into four groups: Control group (I) in which rats were not administrated any treatment. In Groups IIa, IIb, and IIc rats received daily oral omeprazole in dose of 0.75 mg per kg for 2, 4, and 6 weeks, respectively. At the end of the experiment, blood samples were collected for serum creatinine and blood urea nitrogen measurement. Then, animals were sacrificed, and kidney specimens were processed for paraffin blocks, sectioned and stained with H and E, Mallory trichrome and Periodic acid–Schiff, then examined by the light microscope. Stained sections and image analysis were used to count vacuolated cells, pyknotic nuclei, tubular casts, and area percent of collagen fiber deposition, and then, data were subjected to the statistical analysis. Results: Examination of omeprazole-treated groups showed injury of renal corpuscles, renal tubules, and vascular congestion with inflammatory cell infiltrate in renal interstitium. Thickening of basement membrane with deposition of collagen fibers was also detected. Statistically significant increase in the number of vacuolated cells, pyknotic nuclei, hyaline casts, and area percentage of collagen fiber deposition as compared with the control group was noticed, with deterioration of renal function tests. Conclusion: It was concluded that the long-term use of omeprazole resulted in structural damage of rat renal tissue associated with deterioration of renal function in a time-dependent manner.