Background: Duodenal endoscopic biopsy is a common useful test advised for patients presenting with various malabsorption syndromes. Aim:To study the histopathological changes observed in suspected malabsoption cases including Celiac disease (CD) with emphasis upon the Intraepithelial Lymphocytes (IELs) and to have a clinico-pathologic correlation. Settings & Design: This was a 2 year prospective study of cases presenting to gastrology OPD with suspected malabsorption selected for duodenal biopsy. Materials and Methods : Haematoxylin and Eosin (H&E) stain was used for study of histological parameters. IEL counts were correlated in CD3 immunohistochemical (IHC) stain. Clinical and laboratory parameters were correlated wherever available. Statistical Analysis: The variables were expressed as mean ± SD. Chi-square test or independent T test was used for comparison of variables. p value was < 0.05. Results: Out of 164 duodenal biopsies,105 cases had raised IEL.11 patients had CD (10.47%), rest were non celiac disease (NCD) of differen t aetiologies.Liver function tests, Endoscopy, Architecture of mucosa, crypt architecture, blunting, villous crypt ratio showed statistically significant correlation between CD and nonceliac disease groups with p values (P~0.034),(P~0.000),P~0.002),(P~0.000), (P~0,000) and (P~0.000) respectively. The specificity and positive predictive value (PPV) of villous tip IEL in both H&E & CD3 IHC were 100% in CD cases in our study. Conclusion: A complete clinical, endoscopic, serological and histopathological evaluation is essential for diagnosis of CD cases. Raised IEL in duodenal biopsies can be a very useful initial indicator for detecting many latent or subclinical CD cases.