The number of pertussis cases in Japan has decreased dramatically following the nationwide use of an acellular pertussis vaccine combined with diphtheria-tetanus toxoids (DTaP vaccines) which began in 1981. However, the effectiveness of the DTaP vaccine has not been systematically evaluated using appropriate epidemiological methods during a non-epidemic period in Japan. We evaluated the vaccine effectiveness (VE) of the Kaketsuken DTaP vaccine which contains two-component pertussis antigens in Japanese children from 1999 to 2001 using a matched case-control design and data from the Basic Resident Registration and Maternal and Child Health Handbooks. The DTaP vaccination history of 15 children with pertussis and 59 controls was obtained. The VE of 3 or 4 pertussis vaccinations compared with non-vaccination (baseline) was 96·9% for coughing attacks that lasted ⩾7 days, 96·4% for those lasting ⩾14 days, and 95·9% for those lasting ⩾21 days. These findings suggest that DTaP vaccination effectively prevented pertussis during a non-epidemic period in Japan.