Introduction: Marking metastatic lymph nodes before neoadjuvant chemotherapy (NACT) has become increasingly popular in the surgical treatment of breast cancer. A variety of devices are currently in use. However, the significance of lost markers is poorly understood, and their impact on clinical decisions is unclear. Materials and methods: Among participants enrolled in the prospective AXSANA cohort study, those planned for target lymph node biopsy (TLNB) or targeted axillary dissection (TAD) with completed post-NACT locoregional therapy (surgery and radiotherapy) by January 21, 2025, were included. Results: In 88 of 1528 patients (5.8 %), axillary markers could not successfully be removed during surgery after NACT. The lost marker rate differed depending on the marker type (metallic clip/coil 7.0 %, carbon 3.1 %, radar reflector 1.4 %, magnetic seed 0.6 %, radioactive seed 0.0 %, p < 0.001). Additional postoperative imaging was performed in 25 (28.4 %) and further surgery to remove axillary markers was performed in 6 (6.8 %) patients with lost markers. The proportion of patients undergoing axillary lymph node dissection (46.6 % versus 36.5 %, p 0.069) and axillary radiotherapy (51.1 % versus 50.2 %, p 0.748) did not differ between patients with and without lost markers. After an average follow-up of 21.8 months, axillary recurrences occurred in 3 patients (3.3 %) with and 16 patients (1.0 %) without lost markers (rate ratio 2.89, p 0.088). Conclusion: The loss of markers in TLNB/TAD is uncommon and significantly depends on the marking technique. Lost markers may lead to diagnostic uncertainties and additional imaging or surgical procedures.