Background and Aims Novel anti-human epidermal growth factor receptor 2 antibody-drug conjugates (ADCs) have provided new treatment options for breast cancer patients, including those with low HER-2 expression. However, the differences in clinicopathologic characteristics, molecular features, and prognosis between breast cancer patients with low HER-2 expression and those with zero HER-2 expression are still unclear. Therefore, this study was conducted to compare the survival prognosis, clinicopathologic characteristics, and molecular features of breast cancer patients with low HER-2 expression and zero HER-2 expression, in order to further elucidate the molecular characteristics of low HER-2 expression breast cancer and to more accurately identify the population that may benefit from ADC drugs.Methods The data of 1 245 patients with stage Ⅰ-Ⅲ early primary invasive breast cancer who underwent surgical treatment in Xiangya Hospital of Central South University from January 2011 to December 2015 were retrospectively analyzed. The differences in clinicopathologic characteristics among patients with different levels of HER-2 expression (zero expression, low expression, overexpression) were compared. The differences in overall survival (OS) and disease-free survival (DFS) were analyzed, and independent prognostic factors were identified. Molecular characteristics and immune microenvironment differences between low HER-2 expression and zero HER-2 expression breast cancer patients were compared using data from the TCGA database.Results Among the 1 245 patients, 395 (31.73%) had zero HER-2 expression, 562 (45.14%) had low HER-2 expression, and 288 (23.13%) had HER-2 overexpression. Compared to patients with zero HER-2 expression, those with low HER-2 expression had higher lymph node stage, a higher proportion of hormone receptor (HR) positivity, more axillary lymph node metastases, and lower Ki-67 level (all P<0.05). Survival analysis showed that both OS and DFS were significantly lower in patients with HER-2 overexpression compared to those with zero HER-2 expression and low HER-2 expression (all P<0.05); there were no significant differences in OS and DFS between zero HER-2 expression and low HER-2 expression patients, either overall or stratified by lymph node status or HR status (all P>0.05). Multivariate Cox risk model results indicated that age and axillary lymph node metastasis were independent risk factors for OS, while age, ER status, HER-2 expression level, and axillary lymph node metastasis were independent risk factors for DFS (all P<0.05). In terms of molecular characteristics, there were no significant differences in molecular mutation burden between low HER-2 expression and zero HER-2 expression breast cancer, but there were some differences in immune infiltration, with zero HER-2 expression breast cancer exhibiting a more active anti-tumor immune response.Conclusion There are certain differences in the pathological characteristics of low HER-2 expression and zero HER-2 expression breast cancer, but the prognostic outcomes are similar. The molecular characteristics of low HER-2 expression breast cancer are heterogeneous, but do not show significant specificity compared to HER-2 0 expression breast cancer. Therefore, the results of this study do not support the classification of low HER-2 expression as a new molecular subtype of breast cancer.