Rhinoviruses (RV) cause 50% of common colds and are frequently isolated from children and adults hospitalized for asthma exacerbations. Although colds may trigger severe coughing and wheezing, it is not known whether these symptoms are a result of lower airway infection with RV. Previous efforts to address this question by sampling lower airway secretions during experimental RV infections have been complicated by the possibility of contamination of the bronchoscope with nasopharyngeal cells and secretions. To further test the hypothesis that RV infections involve the lower airways, tracheal and nasal secretions were obtained from 23 pediatric tracheostomy patients, including seven with cold symptoms and 16 asymptomatic controls. RV was detected by reverse-transcription polymerase chain reaction from the nasal and tracheal secretions of three of the seven children with cold symptoms. In the 16 well children, RV was not detected in any samples of nasal secretions, but was isolated from four samples of tracheal secretions. These results demonstrate the presence of RV in the lower airways of children with tracheostomies during community-acquired colds, without the possibility of nasal contamination. In addition, these findings suggest that children with tracheostomies carry subclinical viral infections in their tracheas, rather than their noses.