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Abstract Background To investigate the diagnostic reliability of selective microdochectomy after direct ductoscopic wire marking of suspect lesions in patients with pathological nipple discharge. Methods Selective microdochectomy due to pathological discharge was performed in 33 patients with mean age of 51.7 years. Ductoscopes of 0.9 and 1.1 mm in diameter with a channel for wire marking were used. Only patients without sonographic or mammographic correlation for the discharge were included. The pathologic mammary duct was wire marked and extirpated under direct visual guidance via the ductoscope. The histological results were compared with cytology, galactography and ductoscopy. Results In 24 out of 33 cases (72%) an intraductal, epithelial proliferation was found histologically. The following sensitivities for intraductal, epithelial proliferations could be determined: cytology 4%, galactography 74%, and ductoscopy 78%. Conclusion The method allows selective microdochectomy of the pathological duct and the intraductal proliferation under visual guidance. The resection volume can be reduced in contrast to the unselective ductectomy after injection of methylene blue.