Radiofrequency identification tag localization (TL) and magnetic seed localization (MSL) are alternatives to wire localization (WL) for excision of nonpalpable breast lesions. We sought to compare localization methods with respect to operative time, specimen volume, and re-excision rate. A retrospective cohort analysis was performed on TL, MSL, and WL lumpectomies and excisional biopsies at a single institution. Association between localization method and operative time, specimen volume, and re-excision rate was assessed by multiple logistic regression using odds ratios (ORs) and 95% CIs. A total of 506 procedures were included: 147 TL (29.0%), 140 MSL (27.7%), and 219 WL (43.3%). On logistic regression analysis, MSL was associated with longer operative times than WL for excisional biopsies only (OR 4.24, 95% CI 1.92 to 9.34, p < 0.001). Mean excisional biopsy time was 39.1 minutes for MSL and 33.0 minutes for WL. Specimen volume did not vary significantly across surgery types between localization methods. In an analysis of all lumpectomies with an indication of carcinoma, marker choice was not associated with rate of re-excision (TL vs WL OR 0.64, 95% CI 0.26 to 1.60, p = 0.342; MSL vs WL OR 1.22, 95% CI 0.60 to 2.49, p = 0.587; TL vs MSL OR 0.65, 95% CI 0.26 to 1.64, p = 0.359). TL, MSL, and WL are comparable in performance for excision of nonpalpable breast lesions. Although increased operative time associated with MSL vs WL excisional biopsies is statistically significant, clinical significance warrants additional study. With similar outcomes, physicians may choose the marker most appropriate for the patient and setting.