BACKGROUND: Pertussis is an important cause of hospitalization in children. Limited data on pertussis have been reported from China. The aim of this study was to characterize clinically suspected pertussis attributable to Bordetella pertussis among children and determine factors associated with longer duration of hospital stay in B. pertussis infection. METHODS: Two hundred and seventeen consecutive children with clinically suspected pertussis were prospectively enrolled in the study between Jan 2016 through Aug 2017. Variables assessed included demographics, clinical symptoms and laboratory findings. Cox proportional hazards regression model were used to predict variables associated with longer duration of hospital stay. RESULTS: Among the 217 patients with clinically suspected pertussis, B. pertussis was found in 106 (48.8%) patients. Of the 106 children with B. pertussis infection, 63 (59.4%) patients had coinfections with majority due to rhinovirus (HRV) (30.2%), Mycoplasma pneumoniae (29.2%) and human bocavirus (hBoV) (11.3%). Presence of coinfection [odds ratio (OR): 1.73, CI: 1.17-2.54], age </= 3 months (OR: 1.51, CI: 1.09 to 2.27), and WBC count >/=30 x 10(9)/L (OR: 1.66, CI: 1.07 to 2.84) were independently associated with a longer hospital stay. CONCLUSIONS: B. pertussis infection had a high coinfection rate with the majority of coinfections due to HRV, M. pneumoniae and hBoV. Presence of coinfection, Age </=3 months and WBC count >/=30 x 10(9)/L were associated with a longer hospital stay. Children admitted with pertussis need close monitoring when they had evidence of coinfection, Age </=3 months, WBC count >/=30 x 10(9)/L.