This study examined the effects of cage rearing system and backyard raising system on fatty acid profile of egg in laying hens during 9 weeks. Two hundred hens, 70-wk-old, Hy-line Brown, were used in this study and fed basal diets. 100 hens, randomly collected from facility, were transferred to cage rearing system and 100 remaining hens were moved to backyard raising system. For overall period, higher unsaturated fatty acid percentages in two different rearing systems than did saturated fatty acid (SFA) were observed. In unsaturated fatty acid compositions, both rearing system showed a higher mono unsaturated fatty acid (MUFA) contents than poly unsaturated fatty acid (PUFA) contents. Egg quality traits of laying hens reared in backyard system had considerably lower contents of SFA and higher contents of MUFA compared with eggs from cage rearing system (P<0.05). In addition, eggs from cage rearing system resulted in a significantly lower n-3 contents and higher n-6:n-3 ratios and CLA contents in comparison with backyard raising system (P<0.05). However, no significant effects of two different rearing systems on PUFA, PUFA:SFA ratio, and n-6 contents were observed during the experimental period. In conclusion, this result suggests that cage rearing system and backyard raising system will play an important role in improving egg production as functional foods.