Background: Previous studies have indicated that the mechanism of HER2 activation include not only HER2 protein overexpression and gene amplification but also HER2 somatic mutations. The impact of HER2 mutations may be different in HER2-positive (amplified) and HER2-negative (non-amplified) breast cancers. Methods: We used next generation sequencing to detect HER2 mutations in circulating tumor DNA and analyzed the relationship between these mutations and the efficacy of anti-HER2 therapies. Results: Twenty three HER2 somatic point mutations were identified in 16 of the 120 patients (13.3%) studied. HER2 amplified patients with HER2 point mutations have shorter progression-free survival (PFS) compared to non-HER2 mutations, the median PFS was 5.0 months versus 8.4 months. There were three cases identified where HER2 mutation status impacted the selection of personalized anti-HER2 therapies. Case 1 was a HER2 positive patient with an ERBB2 mutation (c.1900T>C/p.C634R) who was resistant to trastuzumab and lapatinib but sensitive to afatinib. Case 2 was a HER2-negative patient with an ERBB2 mutation (p.L755_T759del) was response to afatinib and trastuzumab. Case 3 was a HER2-negative breast cancer patient with two detected mutations in ERBB2 (p.S310F and p.D769Y mutations) who benefited from lapatinib combined with endocrine therapies. Conclusions: Our data suggest that HER2 mutation-positive patients might be resistant to trastuzumab but sensitive to irreversible kinase inhibitors of HER2, whereas HER2-negative patients with HER2 somatic mutations may still be sensitive to anti-HER2 therapies.