Afield experiment was carried out at research station Agriculture College, Abu-Ghraib during the winter season 2006-2007 to study the role of organic fertilization on some characteristics of soil structure and aggregates, and onions yield and some roots anatomy traits. Two sources of manures were used: cow and chicken manure with two levels ( 10% and 20% of soil weight), whereas, chemically fertilized soil with normal practices was regarded as control treatment. Onion cv. Taxas early grano (Sun Seed Co.) transplants were planted on furrows (3 m long and 0.9 m apart) with four lines (i.e. 27 plant. m^-2­­) on 25/11/2006. Field was irrigated as available water drops to 55 % according to soil moisture content weighing method. Plants harvested at maturation on 15/4/2007 and yield of experimental unit were used to calculate yield per Donum (Ton.Donum^-1). Root cross-sections were taken 2 cm from root apices, using freehand sectioning method. Results showed that organic fertilizer application (cow or chicken manures) decreased soil bulk density to 1.29 and 1.30 megagram.m^-3 when applied at level 20%, respectively. Sharp increases were noticed in MWD_w and MWD_d as the level of organic fertilizer increased, indicating its effects on increasing aggregation forces and decreasing the opportunity of dispersion. In addition, the Potential Structure Deformation Index, (PSDI) was decreased by organic fertilization to 22% and 29 % at 10% level, and 23% and 25% at 20% level of cow and chicken manures respectively, compared to 37% of control treatment. Field capacity (FC) and permanent wilting point (PWP) were increased to 0.387 and 0.198 cm³.cm^-3 when cow or chicken manure at 20 % level were added, respectively; compared to 0.318 and 0.161 cm³.cm^-3, respectively of control treatment.  Anatomy test revealed that application of organic fertilizers at 20%, regardless of the source, increased root diameter (1.43 cm), number and diameter of metaxylem and protoxylem vessels to 1.43 cm, 3 vessels, 0.45 and 0.24 mm ; compared to 0.9 cm, 1 vessel, 0.22 and 0.10 mm, respectively for control treatment. The  highest significant onion yield was 6.96 and 6.53 ton.Donum^-1 were obtained when 20% of cow or chicken manure were added compared to 3.84 ton.Donum^-1 of control treatment.