To evaluate the standards of HER2 immunohistochemistry (IHC) interpretation in invasive micropapillary carcinoma of the breast (IMPC). HER2 expression in 60 cases of IMPC was evaluated by IHC and fluorescence in situ hybridization (FISH) using TMA-based techniques. The characteristics between cases with HER2 IHC and HER2 gene amplification results were compared. Using 2007 American Society of Clinical Oncology/College of American Pathologist (ASCO/CAP) criteria, among the 52 cases that were successfully stained by IHC, 40 were HER2 IHC negative and 12 were equivocal (2+). Fifteen cases of HER2 IHC 0 were negative for amplification by FISH. Twenty-five cases with IHC 1+ were tested by FISH; and of these, one showed HER2 amplification, 2 were equivocal, and the others were not amplified. All cases of IHC 2+ showed HER2 amplification by FISH. IHC staining of HER2 was located at cell-cell membrane or basolateral membrane of micropapillary structure, but not in the cytoplasmic membrane facing the stroma in all 13 cases which were HER2 amplified, including 12 showing very strong staining and one showing moderate staining. Among the 37 non amplified HER2 cases, 22 showed IHC staining at cell-cell membrane or basolateral membrane (including 15 weak staining and 7 moderate staining). HER2 IHC detection in IMPC is characterized by staining at cell-cell membrane or basolateral membrane of the micropapillary structure, and absence of staining in the cytoplasmic membrane. It is suggested that interpretation of HER2 IHC staining should be based on membrane staining intensity, but not the completeness of the membrane staining in IMPC. It is suggested to determine the HER2 gene amplification status by using FISH when IHC staining shows moderate or strong intensity.