The persistence of rhinovirus and enterovirus RNAs was studied in the nasal secretions of children with acute expiratory wheezing (median age: 1.7 years). On admission, 84 samples from 161 (52%) children admitted to hospital were positive by reverse transcriptase-polymerase chain reaction (RT-PCR), which detects rhino- and enteroviruses simultaneously. Of the samples, 26 (16%) were positive for rhinovirus, 29 (18%) enterovirus and 29 (18%) nontypable rhino-enterovirus. After 2 weeks, 16 of these 84 (19%) samples were still positive. Rhinovirus RNA remained positive in 13 of 26 (50%) cases, whereas enterovirus RNA remained positive only in 1 of 29 (3%) cases (P = 0.0001). Respiratory symptoms at 2 weeks or systemic glucocorticoid treatment during hospital stay were not related to the persistence of viral RNA. After 5 weeks, only one sample remained PCR-positive. Thirteen of the 79 (16%) asymptomatic control children were PCR-positive for respiratory picornavirus. Five of the 13 (38%) PCR-positive children developed respiratory symptoms in the following week. The study shows that after the onset of symptomatic respiratory infection enterovirus RNA may take 2–3 weeks and rhinovirus RNA 5–6 weeks to disappear from nasal mucus. J. Med. Virol. 72:695–699, 2004. © 2004 Wiley-Liss, Inc.