The research work was carried out to evaluate the acceptability of flaxseed utilization in the baked products. Microwave roasting reduced the cyanogenic glycosides content of flaxseed thus making it fit for human consumption. The partial defattening of flaxseed resulted in the improvement of chemical constituents of flaxseed meal. The flaxseed flours (partially defatted and full fat) supplemented wheat flour significantly improved the chemical composition (ash, crude fat, crude fiber and crude protein) and mineral contents of the composite flours. The chemical constituents remained statistically unchanged during the 60 days of storage studies thus indicating good storage conditions. The mixing time and peak height percentages of the composite flours reduced significantly by the supplementation of flaxseed flour into wheat flour. The scores assigned to all the sensory parameters of chapattis and breads affected significantly with the variation in levels of flaxseed supplementation in wheat flours. The scores for overall acceptability, aroma and taste of chapattis decreased when prepared and tested at 0, 30 and 60 days of flours storage. The scores assigned to all the internal and external sensory attributes of breads decreased by increasing the level of flaxseed supplementation in straight grade flour. The 16% defatted and 12 % full fat flaxseed flours were found the maximum acceptable levels for replacement in chapattis, while in breads 12% replacements of both flaxseed flours resulted in acceptable product. Total, soluble and insoluble dietary fibers, essential amino acid contents and linolenic acid content of chapattis and breads are improved substantially due to the supplementation of partially defatted flaxseed flour or full fat flaxseed flour into wheat flour. True digestibility, NPU, BV and PER of chapattis and breads improved by the supplementation of flaxseed flour. The highest values of TD (84.6), PER (1.87), NPU (54.65) and BV (64.6) were recorded in rats group fed on diets prepared from chapattis containing 16% partially defatted flaxseed flour (PDF). Total cholesterol, glucose, LDL-C and triglyceride contents in rats’ serum decreased due to inclusion of flaxseed supplemented chapattis and breads in their diets. The concentration of HDL improved in the serum of rats fed on diets prepared from flaxseed supplemented chapattis and breads. The diets based on chapattis supplemented with 16% PDF contributed to reduce the serum glucose of rats by 18.16 %, cholesterol by 15.33%, triglycerides by 7.45% and LDL by 18.26%. The HDL concentration of rats serum increased by 7.36% in rats fed on diet prepared from 16% PDF supplemented chapattis. It is proved that flaxseed based bakery products can help to cure and control the cardiovascular diseases in developing countries like Pakistan. It can be advised to public that inclusion of flaxseed in their daily meal plan may be beneficial therapy to control and cure diabetes and cardiovascular diseases.