Background: Evaluation of HER2 in circulating (CTCs) and disseminated (DTC) tumor cells may aid therapy in breast cancer. We report here the discordance in HER2 status in CTCs and DTCs in early stage breast cancer by fluorescence in situ hybridization (FISH) using a microfluidic cell platform (OncoCEE). Methods: Blood (10ml) and BM (1-2ml) from patients with Stage T1 and T2 breast cancer was collected in OncoCEE-Sure collection tubes. Mononuclear cells were recovered using a Percoll density gradient method, incubated with a mixture of 10 primary capture antibodies (Abs), and introduced into streptavidin coated OncoCEE microchannels for tumor cell capture. For blood samples, captured cells were stained with anti cytokeratin (CK) and CD45 Abs for CTC enumeration followed by FISH using probes specific to centromere 17 and HER2. For BM samples, captured cells were subjected to HER2 FISH analysis. The ratio of HER2:CEP17>2.0 in any CK+/ CD45- and CK-/CD45- cell was regarded as positive for HER2. Results: Blood and BM from 68 patients (68 Blood, 54 BM; 54 matched blood and BM) with stage T1N0 (41), T1N1 (6), T2N0 (11), T2N1(2), T2N2 (1), T2N3 (2) with HER2+ (n=7) and HER2- (n=61) breast cancers were studied. The 7 patients with HER2 + primary tumor had HER2+ DTCs in 3/7 (43 %) and HER2 + CTCs in 1/6 (17 %) patients. HER2 + DTCs and HER2 + CTCs occurred in 10/47 (21%) and in 4/57 (7%) patients with HER2- primary breast tumors. The discordance of HER2 status was observed in 14% in CTCs and in 22% in DTCs. Conclusion: 1. The cell enrichment and extraction microfluidic platform (OncoCEE) provides a sensitive approach for evaluation of HER2 in CTCs and DTCs. 2. CTCs and DTCs acquired HER2 gene amplification in 21% and 7% of patients with HER2 negative early stage primary breast cancer. 3. CTCs and DTCs lost HER2 gene amplified status in 57% and 83% of patients with HER2 positive early stage primary breast cancer. 4. The clinical significance of alterations in HER2 status among CTCs and DTCs in early stage breast cancer needs further investigation.