Human epidermal growth factor receptor-2 (Her-2) is a significant prognostic factor and the most important protein in breast carcinoma target therapy. We aimed to evaluate Her-2 gene amplification status detected by quantitative real-time polymerase chain reaction (Q-PCR) with fluorescent in situ hybridization (FISH) as a golden standard, and searched the optimum threshold of Q-PCR when it can be equivalent to FISH. A total of 108 immunohistochemistry (IHC) 2+ invasive breast carcinoma cases from Yunnan province of China were enrolled in this study, assessed Her-2 gene status by FISH and Q-PCR and investigated some clinicopathological variables association with Her-2 amplification results of these two methods individually. A significant correlation of Her-2 FISH results and Q-PCR amplification status with differentiation of lymphatic metastasis (P = 0.001, P = 0.005) was observed and metastasis ratio increased with the rising of mRNA expression. When the cutoff value set at 2.60, compared with FISH, Q-PCR had the same great sensitivity (96.59%), specificity (75%), negative predictive value (94.44%) and positive predictive value (83.33%). This study showed that Q-PCR (cutoff = 2.60) had an extremely good consistency (kappa = 0.739) with FISH and could assess Her-2 status instead of FISH in some cases.