It's a virus. Croup is caused by a virus. Most commonly, the parainfluenza virus. This virus infects the upper respiratory tract, more specifically, the larynx (voice box) and trachea (wind pipe). This is why children with croup end up with a hoarse voice and the telltale barking cough. Cases of croup peak in the fall and winter and are generally most common in children ages 3 months to 3 years.