Objective To study the epidemiological and clinical characteristics of pertussis in infants younger than three months. Methods Infants younger than three months were enrolled from January 1, 2011 to December 31, 2015 with one or more of the following symptoms: persistent cough, spasmic cough, cyanosis of unknown causes, asphyxia and apnea. Multiplex polymerase chain reaction(PCR) assay was performed to identifyBordetella pertussisand enzyme-linked immunosorbent assay was used to detect antibody to pertussis toxin. Clinical features, complications, treatments and prognosis of the infants confirmed with pertussis were analyzed. Results Altogether 202 cases were enrolled in the five years, and 59 (29.2%) of which were positive for pertussis confirmed by multiplex PCR. Among the 59 cases, 37 were boys and 22 were girls. The youngest baby was 13 days and the oldest one was 85 days. Length of stay ranged from 7 to 21 days. Twelve cases had a contact history with family members having chronic cough. Symptoms occurred in spring or summer in 46 cases (78.0%), and in autumn or winter in 13 (22.0%) cases. Symptoms of spasmic cough, cyanosis after coughing, vomiting after coughing and conjunctival hemorrhage were respectively found in 41 (69.5%), 36 (61.0%), 39 (66.1%) and 33 (55.9%) cases, while only six (10.2%) presented with inspiratory whooping sound on coughing. Forty-nine cases (83.1%) showed increased lymphocyte count (≥10×109/L). Twenty-eight cases (47.5%) developed severe pertussis. Complications including apnea and bradycardia after coughing, respiratory failure and heart failure, pertussis encephalopathy as well as highly increased leucocyte count (≥60×109/L) occurred in 23 (39.0%), 18 (30.5%), five (8.5%) and four (6.8%) cases, respectively. Twenty-four cases with severe pertussis required respiratory support, of which six received invasive ventilation and 18 received non-invasive ventilation. Fifty-eight infants were recovered and discharged, while one baby died. Conclusions Bordetella pertussisinfection is an important cause of persistent cough in unimmunized infants under three months of age. The symptoms of pertussis in infants are untypical, but the incidence of severe pertussis is high.Thus early diagnosis and timely treatment are necessary. Key words: Whooping cough; Infant; Cough; Incidence