Objective This study is to evaluate the assay of functional ER by DNA binding analysis and clinical application of RT-PCR for detection of breast cancer micrometastasis to axillary lymph nodes.Methods Protein and total RNA extracted from primary breast cancer and axillary lymph nodes was subjected to perform the gel shift binding analysis and RT-PCT amplifying the Keratin19 fragments respectively. The functional condition of ER was estimated by gel shift binding analysis results combined with hormone binding histochemical assay. The lymph nodes metastasis was assessed referring to the results of both RT-PCR and hematoxylin-eosin (HE) staining. All patients were monitored for tumor relapse during the 3-year follow-up period.Results Among 55 ER positive breast cancer patients. 71% was ERE binding analysis positive. Keratin19 were detected in all 86 breast cancer specimens but not in lymph nodes from patients with benign diseases. Of patients with HE negative staining of lymph nodes, 12.8% (11/86) had significant Keratin19 expression.Conclusion The DNA binding analysis for ER by gel shift can be used as functional ER assay combined with hormone binding histochemical analysis. The expression of Keratin19 in lymph nodes detected by RT-PCR can be regarded as a sign of breast cancer micrometastasis, which conduced to determine the postoperative treatment and predict the prognosis for patients.