Our objective was to identify the association between maternal diet with Chinese herbal medicines and prolonged jaundice of breast-fed infants. Healthy infants at 25 to 45 days of age were eligible for enrollment into this prospective study. Jaundice was defined as a transcutaneous bilirubin (TcB) value ≥ 5 mg/dL. A questionnaire survey asking feeding type, stool pattern, and maternal diet was conducted at the time of TcB measurement. A total of 1148 infants were enrolled, including 151 formula-fed, 436 combination-fed, and 561 breast-fed infants. The incidences of jaundice were 4.0% in formula-fed infants, 15.1% in combination-fed infants, and 39.8% in breast-fed infants (P < 0.001). In addition, jaundice was noted in 37.1% of preterm infants and 25.0% of term infants (P < 0.001). Furthermore, jaundice was more common in breast-fed infants whose mothers did not consume the traditional Chinese herbal medicines than in breast-fed infants whose mothers did consume such medicines (P < 0.001). In conclusion, this cohort study has identified late-preterm birth and breast feeding as the contributory factors for prolonged jaundice of apparently well infants. The data indicate that postpartum diet with Chinese herbal medicines is associated with breast milk jaundice.