RT-PCR assays have been used to analyze expression patterns of atherosclerosis related genes in aorta from 1 to 3-month and liver from 14-day to 3-month old of atherosclerotic model, young apoE deficient (apoE^-/-) mice in normal chow diet. The level of plasma lipids was also analyzed. Combined with the pathomorphological characteristics of the aortic root, the sequential expression characteristics of atherosclerosis related genes in the early stage of the atherosclerosis were studied. ApoE^-/- mice compared with WT mice, the genes detected in the aorta, the expressions of VCAM-1, IκB and TGF-β in 1-month old of the apoE^-/- mice were prominently up-regulated; while the expression of PDGF-α and CD36 were significantly up-regulated in 2-month old, the mRNA levels of TNF-α and MMP2 in 3-month old mice were prominently up-regulated, and IL-1β was significantly up-regulated from 1 to 3-month old. The genes detected in the liver, the mRNA level of CRP was significantly up-regulated at 3-month old of the apoE^-/- mice. The mRNA level of NF-κB had no significant change at different ages in the aorta and liver in the two types of mice. Serum TC, TG and LDL-C levels in different ages of apoE^-/- mice were significantly higher than those of WT mice. It appeared lipid deposition in the intima of aortic root in 2-month old apoE^-/- mice. With the increasing of age, the lesions became more serious. The results implied that the sequential and differential expression of genes related to atherosclerosis formed a complex regulatory network which NF-κB is the core, and the genes may interact with each other and play important roles in the early stages of atherosclerosis of young apoE^-/- mice.