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Background: Real evaluation of any vaccine can only be done after the vaccine has been in routine use for a substantially long period of time. In Japan, acellular pertussis vaccine was introduced and totally replaced whole cell pertussis vaccine in 1981. From 1982 to 1988 40.3 million doses of acellular pertussis vaccine were given to 2-year-olds and from 1989 to 2001 59.3 million doses of acellular pertussis vaccine were given to 3-month-olds. It is now time to evaluate the efficacy and safety of acellular pertussis vaccine by the use of national data officially supplied by the Government.Methods: Government national surveillance of pertussis, which began in 1981, was used to analyze epidemiology of pertussis. Official Government reports on acceptance rates of pertussis were analyzed. A peer review has been made on all severe neurological illnesses/death occurring after pertussis immunization which have been applied for through the Vaccine Injury Compensation System, Ministry of Health Labor and Welfare, Japan.Results: High acceptance rates of acellular pertussis vaccine combined with diphtheria and tetanus toxoids (DTaP) has been maintained and a dramatic decrease in pertussis was noted over the past 23 years. Neurological illnesses temporally associated both with whole cell and with acellular pertussis vaccination has been a rare phenomenon. However, incidences of encephalopathy/encephalitis and status epileptics/frequent convulsions, febrile seizures/provocation of convulsions, and sudden deaths were significantly lower with acellular pertussis vaccination than with whole cell pertussis vaccination.Conclusion: With the use of acellular pertussis vaccine which has been accepted by the public, pertussis has been well controlled in Japan. [ABSTRACT FROM AUTHOR]