Background: Amplification and overexpression of human epidermal growth factor receptor 2 (HER2 /neu) oncogene has considerable prognostic value in breast and gastric cancers. This study aimed to evaluatethe frequency, overexpression pattern, clinical significance, and concordance between the results for proteinexpression and gene amplification of HER-2/neu in gastric and gastro-esophageal junction carcinomas.Materials and Methods: In this study, 101 gastric tissue samples which were included in tissue microarray wereimmunohistochemically examined for overexpression of HER2/neu. Chromogenic in situ hybridization (CISH)was used for HER-2/neu amplification. The correlation of HER2/neu amplification with clinicopathologicalparameters was also assessed. In addition, concordance between CISH and IHC was detected. Results: This studydemonstrated a significant difference in the overexpression of HER2/neu in gastric tumors. The overexpression ofHER2/neu was significantly higher in intestinal type, poorly differentiated grade, large size (5 cm≤) and positivenodal involvement tumors (p-value=0.041, 0.015, 0.038 and 0.071, respectively). Also, amplification of HER2/neuaccording to CISH test, had a significant positive correlation with tumor size and tumor type (p-value=0.018 and0.058, respectively).Concordance between CISH and IHC was 76.9% in 101 evaluable samples. Conclusions:IHC/CISH differences were attributed to basolateral membranous immunoreactivity of glandular cells resultingin incomplete membranous reactivity and/or a higher rate of tumor heterogeneity in gastric cancers comparedto breast cancers. Therefore, this can be a potential marker for targeted therapy of malignant gastric tumors.