WU polyomavirus (WUPyV), a new member of the genus Polyomavirus in the family Polyomaviridae, has been found to be associated with respiratory tract infections recently. But the role of the WUPyV as agents of human disease remains uncertain. We sought to describe the detection and clinical characterization of WUPyV in acute respiratory tract infection in children.From July 2008 through June 2009, nasopharyngeal aspirates were collected from 771 children who were hospitalized with acute respiratory tract infection in Second Affiliated Hospital of Shantou University Medical College, and from 82 asymptomatic children who visited the health checkup clinic. WUPyV was detected by using PCR technology and was identified by using DNA sequencing. All WUPyV-positive specimens were screened for 9 common viruses [influenza A and B, respiratory syncytial virus (RSV), parainfluenza virus (PIV) 1 and 3, human metapneumovirus, human bocavirus, adenovirus and rhinovirus] by using PCR or RT-PCR. The clinical data of WUPyV infection were collected and analyzed.In this study, fifteen of the 771 tested specimens with acute respiratory tract infection were positive for WUPyV, the positive rate was 1.95% and all of the asymptomatic children who visited the health checkup clinic were negative. Of the 15 cases who were positive for the virus, the age range was 2 to 48 (mean 18.8) months, 9 (60%) were male and 6 (40%) were female. WUPyV was the sole virus detected in 9 specimens (60%) from patients with acute respiratory tract infection. WUPyV was associated with the co-infection with another respiratory virus in 6 of 15 (40%) cases, most frequently with RSV (n = 4), followed by adenovirus (n = 1) and rhinovirus (n = 1). The most common clinical findings in the patients with WUPyV were cough, fever and wheezing. The most frequent diagnoses were pneumonia (n = 8), bronchiolitis (n = 4), upper respiratory tract infections (n = 2) and bronchitis (n = 1). A severe case was complicated with viral encephalitis.WUPyV may be a respiratory pathogen because it was the sole virus detected in 9 specimens from patients with respiratory illness and all of the asymptomatic controls were negative. The most common clinical findings are cough and wheezing. Young children may be susceptible to infection with this virus and occasionally the infection with this virus may cause severe disease. More comprehensive and in-depth studies are required to prove the pathogenicity of these viruses.