Croup is usually caused by a viral infection with parainfluenza virus, respiratory syncytial virus (RSV), or influenza viruses A and B. These viruses are commonly present in the air, especially during the late fall and winter. One bacterium that can cause croup is Hemophilus influenzae.

Croup occurs most often in children between 6 months and 3 years of age.

The characteristic barking cough and noisy breathing (stridor) is caused by swelling in the upper airway (larynx, trachea, and bronchi). The child's breathing becomes more difficult and requires increasing physical effort. The child may be physically tired but is unable to rest because of the increased breathing effort.

The child may be restless, have a fever, and be working hard to keep breathing. Extra effort to breathe may be noticed as wider opening of the nostrils during inhalation (nasal flaring); increased use of the muscles in the neck and chest; and unwillingness to lie down, rest, eat, or drink. In severe cases the child's lips and fingers may turn blue (cyanosis), indicating inadequate oxygen supply.

In severe cases of croup, there may also be a bacterial super-infection of the upper airway. This condition is called bacterial tracheitis and requires hospitalization and intravenous antibiotics. If the epiglottis becomes infected, the entire windpipe can swell shut, a potentially fatal condition called epiglottitis.