Correct preoperative diagnosis of a breast lesion is essential for optimal treatment planning. Our aim was to compare feasibility of fine needle aspiration cytology (FNAC) and core needle biopsy (CNB) in diagnosis of breast lesions. The special aim was to evaluate the extra costs and delay in surgical treatment due to unsuccessful preoperative biopsies. Diagnostic work-ups in 572 patients with 580 breast lesions were retrospectively evaluated. FNAC was the first biopsy method for 339 lesions, CNB for 241 lesions. The postoperative diagnosis was malignant for 503 lesions. The preoperative rate of definitely malignant diagnosis was 67% (194/289) for FNAC and 96% (206/214) for CNB (p < 0.0001), and 95% and 99%, respectively (p = 0.0173), when also suspicious findings were included. In patients with FNAC, an additional needle biopsy was performed for 93 and a surgical biopsy for 62 lesions. In the CNB group, a subsequent CNB was performed for 2 and a surgical biopsy for 33. The frequent need for additional biopsies raised the total expenses of FNAC over those of CNB. Multiple biopsies may also delay cancer surgery. It is therefore recommended to use CNB as the initial needle biopsy method.