Background: Evaluation of HER2 status of circulating tumor cells (CTCs) and disseminated tumor cells (DTCs) can provide valuable information to make therapy changes. We report here the utility of a microfluidic platform for evaluation of HER2 gene amplification in CTCs and DTCs by fluorescent in situ hybridization (FISH). Methods: Blood (10ml) and BM (1–2ml) were collected from patients with operable breast cancer. Mononuclear cells were recovered, incubated with a mixture of 10 primary capture antibodies(Abs), introduced into CEE microchannels ( Biocept, Inc,San Diego), stained with fluorescent cytokeratin (CK) and CD45 Abs and then processed for FISH using probes specific to centromere 8 (spectrum aqua), 17 (spectrum green) and HER2 (spectrum orange). The ratio of HER2:CEP17 >2.2 in any CD45 negative cell was regarded as positive for HER2 gene amplification. Results: Blood and BM from 50 patients with T1N0(26),T1N1(5),T2N0(6),T2N1 (3),T2N3(3),T3N0 (2),T3N1(1),T4N1(2),T4N3(2) with 7 HER2+ and 43 HER2 - invasive tumors were studied. HER2+ CTCs were noted in 4/49 (8.0%) patients with HER2 + (1) and HER2 - (3) tumors. HER2+ DTCs were noted in 14/50 (28%) patients with tumors that were HER2+ in 2 and HER2- in 12 patients. Six of the 7 patients with HER2 amplified tumors did not show any HER2 amplified CTCs and 5 of the same patients did not contain HER2+ DTCs. Overall, HER2 gene amplified CTCs and DTCs were noted in blood and BM simultaneously in only 2 patients and in either the blood (2) or BM (12) in the remaining patients. Conclusions: 1. The cell enrichment and extraction microfluidic technology (CEE) provides a sensitive platform for evaluation of HER2 by FISH in intact CTCs and DTCs. 2. HER2 + CTCs and DTCs were encountered in HER2 + as well as in HER2 - primary tumors. 3. Discordant HER2 status was contributed mainly by HER2 + DTCs occurring in HER2 -primary breast tumor. 4. The clinical implications of evaluating HER2 in CTCs and DTCs in patients with invasive breast cancers needs further investigation.