Breast cancer is one of the most common diseases in females, arising from overexpression of a variety of oncogenes like HER2/neu. The amplification rate of this gene is variable in different breast cancer patients. In this study, the amplification of the HER2/neu oncogene was distinguished in breast cancer patients and its correlation with prognostic factors. Also, the simultaneous effect of prognostic factors on the occurrence of a specific prognostic factor was investigated. The multiplex PCR technique was used to assay the amplification of the HER2/neu oncogene in breast cancer patients. After extracting DNA from 100 tumor tissue and 8 normal breast tissue samples, the amplification of the HER2/neu gene was distinguished by the co-amplification of a single-copy reference gene, γ-IFN, and the target gene HER2/neu in the PCR reaction and using the Gel analyzer software. SPSS 23 and STATA 9.1 software were used for statistical analysis. The HER2/neu gene was amplification in 30% of the tumor samples. The statistical analysis showed a statistically significant relationship between HER2/neu gene amplification and progesterone receptors. Amplification of the HER2/neu gene significantly increases the chance of lymph node involvement. Also, the amplification of this gene in tumors with histological grade II tissue is more than grade I. The amplification of the HER2/neu gene can be used as an independent prognostic factor in predicting lymph node involvement and histological grade in breast cancer patients.