The aim of this study was to develop functional bread enriched with omega-3 fatty acids. High amylose corn starch was used to form nanosized complexes with flax seed oil that was converted to powder of microparticles by spray drying. The particles were then incorporated into bread formulation at different amounts to investigate their effects on bread quality characteristics. The effects of encapsulation on the formation of lipid oxidation products and thermal process contaminants including acrylamide and hydroxymethyl furfural (NW) were determined. Encapsulation significantly decreased lipid oxidation as measured by the formation of hexanal and nonanal in breads during baking. Increasing the amount of particles in dough significantly decreased the formation of acrylamide and HMF in breads. Scanning electron microscopic analysis of bread demonstrated that particles added to dough remained intact in the crumb, but partially destroyed in the crust. Comparing to its free form, addition of nanoencapsulated flax seed oil increased final product quality and safety by lowering lipid oxidation and formation of harmful compounds in breads during baking. (C) 2011 Elsevier Ltd. All rights reserved.