Background The clinical significance of the presence of more than one type of virus in the respiratory specimens of children with respiratory infections is not clear. Objectives To describe the clinical characteristics of multiple viral infections versus single infection by respiratory syncytial virus (RSV) in hospitalized infants. Study design This is a prospective study conducted in all infants under 2 years of age admitted for acute respiratory infection (September 2000–June 2003) in a secondary teaching hospital. Virological diagnosis was made by two different multiplex reverse transcription-nested polymerase chain reaction (RT-PCR) assays in nasopharyngeal aspirates. We describe the clinical characteristics of the patients with multiple viral infections and compare them to a group of 86 randomly selected patients infected only with RSV. Results 749 specimens taken were analyzed. Respiratory viruses were detected in 65.9% of the samples. 86 children had multiple viral infections (17.4% of all positive specimens). The most frequent clinical diagnosis in this group was recurrent wheezing in 44% and bronchiolitis in 52%. Fever was significantly more frequent ( p < 0.001), hospital stays were longer ( p = 0.05), and antibiotic treatment was used more ( p = 0.03) in infants with multiple viral infections than in the RSV-infected group. Conclusions Multiple viral infections are frequent in hospitalized children with respiratory tract disease (17.4%). Multiple viral infections are linked to higher fever, longer hospital stays and more frequent use of antibiotics than in the case of infants with single RSV infections.