Different housing systems have considerable influence on performance in poultry production. Therefore, the present study was undertaken to investigate the impact of different housing systems on the performance, bone mineral density and egg yolk fatty acid composition in laying hen. Hy-line brown pullets (n=450) of 12 weeks age were randomly divided into 3 housing systems with 6 replicates of 25 birds in each room. A diet with 2,750 kcal/kg ME and 16.5% CP was assigned to all birds. The pullets provided free access to feed and water. Significantly (P<0.05) higher values for egg production, egg mass and feed conversion efficiency were found in battery cages, however egg weight, egg shell color and breaking strength was remarkably (P<0.05) higher in floor system. The albumin height and Haugh unit were significantly higher (P<0.05) in battery cages which was statistically similar to aviary housing system. The egg yolk fatty acids concentration of linoleic acid and linolenic acids were significantly higher in aviary and in floor system, respectively, however both values were lower in battery cages. Saturated and unsaturated fatty acid content (%) in egg yolk did not influence by any housing systems. Bone mineral density was significantly higher (P<0.05) in floor and aviary housing system than that of battery cage system. It was concluded that in battery cages the egg production and composition maximized, however higher bone mineral density and yolk fatty acids content can be improved in the laying hen reared on floor and aviary housing systems.