Development of bakery products containing milled flaxseed, could have potential health benefits due to its high antioxidant, lignan and omega-3 fatty acid alpha linolenic acid content. However the effect of adding flaxseed, especially in the high amounts required for use as the food supplement in clinical trials, may affect the flavor characteristics. The objective of this study was to evaluate the flavor profile of different muffin and snack bar formulations with and without milled flaxseed. Three snack bar formulations and two muffin formulations with and without flaxseed were evaluated by ten and eleven trained assessors respectively. The intensity of seven aroma and eight flavor attributes for snack bars, and nine aroma and ten flavor attributes for muffins were measured on 15-cm line scales. Both the orange cranberry and apple spice muffin formulations with flaxseed had significantly lower sweetness and vanilla aroma and flavor intensities, and significantly higher grain/flax aroma and flavor, and bitter taste compared to the non-flax muffin. Of the two flavorings apple spice appeared to have the best potential, since the apple aroma and flavor were significantly higher for the flax muffin compared to the non-flax muffin. The orange cranberry, gingerbread raisin and cappuccino chocolate chip snack bar formulations with and without flaxseed showed no significant differences in intensities for the grain/flax aroma and flavor. The gingerbread raisin snack bar formulations showed no significant differences for any other attributes except for higher spice aroma in the flax sample, which makes it a promising flavoring option.