Comparative studies are useful in the prediction of validated 3D structure of a query protein (Amylase). Modeler is used for structure prediction of amylase. All the structural models are verified by results of ramachandran plot, Whatif server, Prosa (ll) and Procheck (Checks the stereochemical quality of a protein structure, producing a number of postscript plots analyzing its overall and residue-by- residue geometry. Predicted and validated structure (after comparative study) is useful in structure based drug designing, protein-DNA interactions, study of protein-protein interactions and protein-ligand binding. Amylase is an enzyme that breaks down starch into sugar. Amylase is present in human saliva, where it begins the chemical process of digestion. The pancreas also makes amylase (alpha amylase) to break down dietary starch into disaccharides which are converted by other enzymes to glucose to supply the body with energy. There are 3 subunits of amylase, α, β and γ. A higher than normal concentration may reflect one of several medical conditions, including acute inflammation of the pancreas, macroamylasemia and perforated peptic ulcer, urine and blood amylase levels may also be elevated with a variety of other conditions, such as ovarian cancer, lung cancer, tubal pregnancy, mumps, intestinal obstruction, or perforated ulcers. Key words: Amylase, ramachandran plot, stereochemical, 3D structure, modeler.