Introduction: In India particularly in Rajasthan state, peoples drink water having high level of nitrates and concentration up to 500 mg of nitrate ion per liter is common. The ingested nitrate is converted to nitrite in the digestive system and absorb in blood causing methemoglobinemia. The peak of methemoglobin is observed at 45–95 mg/Liter of nitrate concentration of water. Aim of study: To find out the correlation between drinking water nitrate concentration and histopathological changes in duodenum and jejunum of rabbits of different groups. Materials & Methods: An experimental study was conducted in 10 rabbits according to guideline of ICMR, New Delhi between three and a half months to four months of age having weight ranging from 1.310 kg to 10720 kg. Five groups A, B, C, and D & E were formed with two rabbits in each group. The control group A was given water orally having 06 mg/ liter. Groups B to E (experimental groups) were administered water orally having a concentration of 100 mg/Liter, 200 mg/Liter, 400 mg/Liter & 500 mg/Liter of nitrate respectively for 120 days. Then all rabbits were anaesthetized and sacrificed according to the guidelines of the ICMR and duodenum and jejunum were removed and processed for paraffin sections. Hemotoxyllin and eosin staining was done for microscopic observations. Results: The results showed mononuclear infiltration and ulceration of epithelium in mucosa of duodenum and jejunum which started in Group B. The histopathological changes appeared in sub-mucosa, muscularismucosa, muscularisexterna and serosa, started from Group C as exfoliation, crowding and stratification of epithelium. The changes were more pronounced in duodenum and jejunum of group D & E in the form of congestion of blood vessels in sub mucosa and mild infiltration of lymphocytes in muscularisexterna and abnormal villi.