WebMD reports that coughing up brown mucus or phlegm generally points to a small amount of blood contaminating the mucus. Most blood in mucus comes from the nose, according to WebMD, but coughing up brown mucus usually indicates that the blood is coming from the throat. HealthStatus warns that a significant number of blood particles in phlegm can potentially point to a serious lung infection.
According to SinusWars, coughing up brown mucus can be a sign of numerous conditions, including exposure to dirt in the air, cigarette smoking and damage to the lining of the nasal cavities. When dirt and dust particles in the air are breathed in, the mucus traps and takes on the coloration of the contaminant. For example, cigarette smokers often cough up brown mucus as a result of the dark cigarette smoke tingeing their mucus. SinusWars also explains that the lining of the nasal cavities is extremely delicate and begins to crack and bleed with minor irritation, resulting in brown-tinged mucus.
According to HealthStatus, heavy air pollution is also a significant cause of brown mucus. Bacterial infections may also cause mucus to take on a greenish-brown tint that varies in color from one individual to another.