Introduction: The vacuum-assisted biopsy (VAB) and the Breast Lesion Excision System (BLES) are minimally invasive biopsy techniques, both used as diagnostic and therapeutic tools. The aim of the study is to compare these two methods and assess them in the context of discomfort, early and late complications and their diagnostic and therapeutic potential. Material and methods: The study involved 173 patients who underwent a VAB or a BLES breast biopsy in the period between 2009 and 2016. Approximately 3 months after the biopsy, the patients completed a questionnaire in which they assessed the procedure for discomfort associated with the procedure and the final cosmetic outcome. The cosmetic effect of the biopsy was also assessed by a surgeon. Results: The BLES and the VAB breast biopsies did not differ in terms of pain, duration, and discomfort of the procedure, breast bruising, breast tenderness about 24 h after the procedure or pain lasting over 3 months after the biopsy. Subsequently, the biopsies were evaluated in terms of the cosmetic effect assessed by the patient and by a surgeon and no differences were observed. There were no significant differences between the VAB and the BLES breast biopsies in the course of the procedure, early and late complications and cosmetic effect. Conclusions: Since the BLES breast biopsy makes it possible to evaluate the margins, it is a good alternative to the open breast biopsy.