This study aimed to explore the positive rate of non-visualized sentinel lymph nodes (non-vSLN) [1] in breast cancer (BC) patients and the discrepancy of non-vSLN among different molecular subtypes, in order to further evaluate the clinical risk of non-vSLNs. A total of 627 patients were retrospectively analyzed. These patients were pathologically confirmed with invasive breast cancer and underwent sentinel lymph node biopsy (SLNB). Various factors were compared using chi-square test. The positive rate of SLNs between non-vSLNs and visible sentinel lymph nodes (vSLNs) were compared. Moreover, factors that influenced the prognosis, such as ER, PR, HER-2, histological grade and lymph node metastasis were compared between these two groups. Among the 627 patients who underwent SLNB, 196 patients had non-vSLNs, accounting for 31.26% (196/627) and 113 patients had positive SLNs, accounting for 18.02% (113/627). Furthermore, 40.71% (46/113) of patients with positive SLNs had non-vSLN, and 17.39% (8/46) of patients with non-vSLN had HER-2+BC. In contrast, 35.82% (24/67) of patients with vSLNs had HER-2+BC. Moreover, 23.91% (11/46) of patients with non-vSLN and 5.97% (4/67) of patients with vSLNs had triple-negative breast cancer (TNBC). The metastasis rate was 41.30% (19/46) in the non-vSLN group and 43.28% (29/67) in the vSLN group. The difference in the rate of positive SLNs between the non-vSLN and the vSLN groups was statistically significant (P< 0.05), in which the positive rate of SLNs in the non-vSLN group was remarkably higher than that in the vSLN group. The differences in the proportion of HER-2+BC and TNBC between the non-vSLN and the vSLN groups were statistically significant (P< 0.05), in which HER-2+BCwas evidently higher in the vSLN group than in the non-vSLN group. Meanwhile, TNBC was markedly higher in non-vSLN group than in the vSLN group. Furthermore, differences in Luminal A subtype, Luminal B subtype and non-SLN metastasis between these two groups was not statistically significant. In addition, the difference in non-SLN metastasis rate was not statistically significant among breast cancers of different molecular subtypes and between the non-vSLN and the vSLN groups. Breast cancer patients with positive non-vSLNs are more likely to have a TNBC subtype relative to patients with positive vSLN. Breast cancer patients with non-vSLN have higher positive rate of SLNs. The non-SLN metastasis rate in positive SLN patients was not correlated to the molecular subtype of breast cancer.