This study aimed at assessing the effects of supplementing diet of laying hens with different Se sources (inorganic and organic), as antioxidant factor, and omega-3 fatty acids from flaxseed source, as oxidant factor on egg Se and omega-3 antioxidant status of yolk. In a completely randomized design, 384 "Hy-Line W36" hens were assigned to a 3×4 factorial arrangement comprising four replicates of eight, for ten weeks. Birds received three basal diets containing 0, 5% and 10% of flaxseed supplemented with no additional Se (SN), and Se from sodium selenite (SS), Se-enriched yeast(SY) and hydroxy seleno-methionine(SOH). Inclusion of flaxseed decreased egg weight and egg mass. Egg physical qualities were not mostly affected by flaxseed. Neither effect of Se sources nor interaction effect was observed on the egg physical qualities. Using any forms of Se improved GSH-Px activity and just organic forms improved TAC. Moreover, flaxseed in diets resulted in a lower level of oleic, linoleic and arachidonic acids level and higher ALA, DPA and DHA in yolk. Indices such as MUFA, Σn-6, n-6:n-3 ratio, SFA:n-3 appeared to drop, while PUFA and Σn-3 rose. Organic Se sources especially SOH turned out to cause better deposition of Se in both yolk and albumen.