1. What does it mean when a baby coughs with phlegm? In winter, many babies will have a cough, sometimes accompanied by phlegm. This may be caused by a cold or other reasons. If your baby coughs and produces phlegm, timely measures need to be taken for treatment. 2. Causes of babies coughing with phlegm 1. Caused by colds: Colds are one of the most common causes of babies coughing with phlegm. Colds can lead to infection of the respiratory tract, causing inflammation and increased secretions. 2. Bronchitis: Bronchitis can also cause cough and phlegm in babies.