This study was undertaken to compare the cost effectiveness of two vacuum-assisted breast biopsy devices, the Mammotome and Vacora systems. Between January and June 2006, 238 vacuum-assisted breast biopsies were performed at our radiology department. Five out of 238 lesions were excluded because of inadequate sampling. The Mammotome system was used in 108/233 lesions and the Vacora system in 125/233. Fifty-eight lesions underwent ultrasound-guided breast biopsy, and 50 lesions underwent mammography-guided biopsy with both Mammotome and Vacora devices. Magnetic-resonance-guided biopsy was possible with the Vacora system only (17/125 lesions). All procedures were successfully completed. No significant differences were found between the results of the Mammotome and Vacora biopsies in terms of effectiveness: sensitivity was 84.4% and 86.2%, respectively, and specificity 100%. In terms of cost, the Mammotome system has higher costs per procedure compared with the Vacora. Our clinical results confirm the diagnostic accuracy of both the Mammotome and Vacora systems, whereas our cost analysis shows that there is a considerable difference, mostly related to the initial investment.