Beneficial effects of polyunsaturated fatty acids on health as well as their high susceptibility to oxidative deterioration have promoted the development of different delivery systems. In this research, alpha-linolenic (omega-3) and linoleic (omega-6) essential fatty acids obtained from enzymatic hydrolysis of chia seed oil, were incorporated into high amylose starch by inclusion complexation, studying the effect of time (2 and 6 h) and temperature (50, 70 and 90 degrees C) of crystallization on the physicochemical properties of the obtained complexes. Results showed a mass yield that ranged from 62 to 72% and the X-ray diffractograms confirmed the formation of a typical V-amylose pattern. Amylose-lipid complexes presented a high omega-3 and omega-6 fatty acid content (2.4-3.1%) and broad melting endotherms whose peak temperatures were in the range of 85-95 degrees C, exhibiting an increase as the crystallization temperature rose. The microstructure showed that the inclusion complexes were composed of irregular-shaped solid clumps. Thermogravimetric analysis displayed a mass gain in the uncomplexed fatty acids associated with lipid oxidation, while there was no evidence of this behaviour for the amyloselipid complexes. The final properties of these systems were mostly influenced by the temperature rather than by the crystallization time. Therefore, the results suggest that these complexes could be used as a potential delivery system of essential fatty acids in thermally-processed foods.