Background The most common cause of pathological nipple discharge (PND) is single papilloma, which is a benign intraductal lesion (BIL). However, underlying malign (MIL) or high-risk intraductal lesions (HIL) should be considered during examination. Aim To reveal the value of conventional imaging methods (CIM), discharge characteristics, and cytology in lack of intraductal imaging methods to detect intraductal lesions (IL) and MIL that cause PND. Methods We compared the pathological findings with the characteristics of discharge, CIM, and cytology findings of the patients who admitted to our clinic with nipple discharge and underwent duct excision (n = 111). Results IL were detected in 69 (62.2%) patients as BIL (n = 31), HIL (n = 23), and MIL (n = 15). Most of the IL was observed with bloody, serosanguineous, and serous discharges (83.3%, 76.2%, and 69.2%, respectively). The sensitivities of ultrasonography, MRI, and cytology in detecting IL were found to be 50.7%, 42.6%, and 74.1%, while their specificities were found to be 73.8%, 88.2%, and 48.6%, respectively. None of the CIM was sufficient to detect MIL in 5 (33.3%) patients. The appearance of red blood cells detailed in cytology was significantly related to IL (p < 0.01), whereas the presence of inflammatory cells was related to ductal ectasia and periductal mastitis (p < 0.001). Conclusions Although patients' physical examinations, CIM, and cytology findings were normal, duct excision procedures should be applied to exclude MIL or HIL, which can be a cause of discharge in case of suspicious color. The details in cytology reports have a role in increasing the value of cytology.