Whole sunflower seeds were exposed to microwave roasting for 6, 12, 20 or 30 min at a frequency of 2450 MHz. The kernels were then separated from the sunflower seeds, and the lipid components and the positional distribution of fatty acids in triacylglycerols (TAGs) and phospholipids (PLs) were investigated. Major lipid components were TAGs and PLs, while steryl esters, free fatty acids and diacylglycerols were also present in minor proportions. The greatest PL losses (p <0.05) were observed in phosphatidyl ethanolamine, followed by phosphatidyl choline or phosphatidyl inositol. Significant differences (p <0.05) in fatty acid distributions occurred (with few exceptions) when sunflower seeds were microwaved for 20 min or more. Nevertheless, the principal characteristics for the positional distribution of fatty acids still remained after 20 min of microwave roasting; unsaturated fatty acids, especially linoleic, were predominantly concentrated in the sn-2-position and saturated fatty acids, especially stearic and palmitic acids, primarily occupied the sn-1- or sn-3-position. These results indicate that no significant changes in fatty acid distribution of TAGs and PLs would occur within 12 min of microwave roasting, ensuring that a good-quality product would be attained.