Introduction: Gastrointestinal malignancies are on raise and there is a need for predictive and prognostic markers to study the tumor behavior. In the present study we have evaluated four most important markers in these tumors in Indian population so that drugs targeting these proteins can be included in the therapeutic regimes. We also compared the expressions with the grade and stage of the tumors. Materials and methods: The present study is an observational cross-section study. We have included neoplasms of Stomach, Colon and Rectum, 30 benign and 30 malignant neoplasms from each organ. Results: HSP90 expression was associated with the grade and stage of all tumors except grade of colonic tumors. HER2 was associated with grade and stage of all tumors except stage of stomach & rectum and grade of carcinoma colon. Ki-67 expression was associated with grade and stage of all tumors except stage of rectal carcinoma. p53 is associated with grade and stage of all the tumors. Conclusion: Marked geographical variations have been identified in the phenotypic characters of the tumors. An understanding of the pattern of expression of prognostic and predictive markers shall be helpful in better analysis of the tumor behavior.