Purpose To explore the application for clinical assessment of HER2 gene expression status by chromogenic in situ hybridization (CISH) and to compare the results with those obtained by immunohistochemistry(IHC). Methods CISH for HER2 gene expression status was performed using SPOT-Light HER2 CISHTM on the archival paraffin-embedded sections of breast cancer tissues from 40 cases with immunohistochemical staining scores of (+++),(++),(+) and (-). Results Of the 8 cases with score (+++) by IHC,7 cases showed HER2 gene amplification by CISH,1 case CISH-negative. Five of the 13 cases with score (++) showed HER2 gene amplification,the remaining 8 cases were CISH-negative. Two of 10 cases with score (+) showed HER2 gene amplification,the remaining 8 cases were CISH-negative. All the patients with scores negative (n=9) failed to show amplification. Certain difference to the examination of HER-2/neu status (kappa=0.458,P=0.003) was found in the kinds of method. Conclusion Immunohistochemistry(IHC) is the first choice in primary screening for HER2 expression status. Because of the obvious discrepancies between protein expression and gene amplification,patients with score (+++~+) by IHC should undergo CISH testing.