We examined pertussis hospitalizations among infants aged <1 year between 2006 and 2008 using the nationwide inpatient database in Japan. A total of 660 infants hospitalized for pertussis were identified. Peak incidence occurred at age 1 month and infants aged 0-2 months (too young for pertussis vaccination) and ≥3 months (eligible for at least one dose of vaccination) accounted for 44·5% and 55·5% of hospitalizations, respectively. Complications related to pertussis were found in 165 (25·0%) cases, including one death; the age at admission did not differ significantly between patients with and those without complications (mean age 4·1 vs. 4·5 months, P=0·12). Seventeen patients required mechanical ventilation. Of the 17 cases, 14 infants were aged <3 months and three infants were aged ≥3 months. Our findings highlight that the vaccination schedule against pertussis may often be delayed in Japan.