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Background Our previous study showed that the combined Chinese herbs containing scutellaria baicalensis georgi and gardenia jasminoids ellis inhibited atherosclerosis. In this study, we sought to determine if baicalin and geniposide could inhibit atherosclerosis through Wnt1 and dickkopf-related protein-1 (DKK1). Methods The wild-type and ApoE−/− mice were treated with baicalin, geniposide, and baicalin plus geniposide daily by gavage for 12 weeks. Blood lipid levels were measured with an automatic biochemistry analyzer. Aortic atherosclerotic lesion areas were analyzed with Image-ProPlus software. The mRNA and protein expression of DKK1, Wnt1 and nuclear factor-κB (NF-κB) were measured with RT-PCR and Western Blot. Serum levels of interleukin-12 (IL-12) were quantified with ELISA. Results The baicalin or geniposide monotherapy as well as combination therapy inhibited the development of atherosclerotic lesions, increased Wnt1 and decreased DKK1 expression and elevated the ratio of Wnt1/DKK1 compared with high-lipid diet group. However, only baicalin or geniposide monotherapy decreased NF-κB expression. Moreover, baicalin and geniposide mono- or combination therapy lowered IL-12 levels. Geniposide reduced both serum total cholesterol and low density lipoprotein levels, while baicalin either alone or in combination with geniposide did not affect serum lipid levels. In human, umbilical vein endothelial cells stimulated by oxidized low density lipoprotein, baicalin and geniposide also increased Wnt1 and decreased DKK1 expression and elevated the ratio of Wnt1/DKK1. Conclusions Baicalin and geniposide exert inflammation-regulatory effects and may prevent atherosclerotic lesions through enhancing Wnt1 and inhibiting DKK1 expression.