A capillary electrophoresis immunoassay (CEIA) method based on enhanced chemiluminescence (CL) detection was developed and applied to arteriosclerosis pathology research in the medical field. The system of enzyme-horseradish peroxidase (HRP) catalyzing the luminol/H2O2/p-iodophenol reaction was adopted in this paper. HRP was detected with the detection limit (S/N = 3) of 4.4 pM (53 zmol), which represents one of the highest sensitivities of HRP reported yet. HRP was first linked to bone morphogenic protein-2 (BMP-2) in rat vascular smooth muscle (VSM) cells with noncompetitive format and analyzed by CE-CL. HRP-Ab(2)-mAb-BMP-2 complexes can be baseline separated from free HRP in 3 min. The detection limit (S/N = 3) of BMP-2 is 6.2 pM (75 zmol). This technique has been successfully applied to arteriosclerosis development mechanistic study by investigating the change of BMP-2 content in VSM cells, which were stimulated by angiotensin II for different times. The change trends of BMP-2 contents are well in accord with that of the commonly used pathology image analysis system. It proves that the CEIA-CL technique proposed could be developed into a sensitive and new method for clinical assay and pathology research.