Unilateral single-duct nipple discharge is associated with an increased risk for underlying breast malignancy. There is no consensus whether color of nipple discharge independently indicates the risk of malignancy. We sought to assess the relationship between the color of discharge and the risk of malignancy. Patients with unilateral single-duct nipple discharge without abnormalities on clinical and radiologic examination were included. Prior to diagnostic microdochectomy nipple discharge characteristics were registered. Multiple logistic regressions were performed to assess the relationship between color of nipple discharge and malignancy, corrected for age. During a mean follow-up period of 7.1 years we determined complication rate and false-negative rate of microdochectomy. A total of 184 patients were included (median age 53 years, range 19–84). Histologic examination revealed (in situ or invasive) breast carcinoma in 10.9% (20) of patients and high-risk lesions in 11.4% (21). Malignancy or high-risk lesions were found in 25% (OR: 1.37; 95% CI: 0.62–3.00) of patients with bloody discharge. Risk of underlying malignancy increased in patients >60 years (OR: 2.35; 95% CI: 1.14–4.83). Complication rate of microdochectomy was 2.7%. Single-duct, unilateral nipple discharge is a sign of underlying malignancy in a substantial proportion of cases. The majority of patients with unilateral single-duct nipple discharge, diagnosed with breast cancer, present with bloody discharge. However, the association between bloody nipple discharge and malignancy is not strong enough to distinguish high-risk patients. Therefore, invasive diagnostic procedures like microdochectomy should be offered to all patients with unilateral uniductal nipple discharge to search for underlying malignancy.