Whole-cell Pertussis (wcPertussis) vaccines combined with diphtheria and tetanus toxoids are effective in preventing clinical pertussis. The study aimed at determining the cost of managing fever and convulsions and cost of adverse events associated with wcPertussis. Parents who brought their children to health clinics and parents of children who were admitted for febrile convulsions were interviewed using structured questionnaire and the information were used to determine the cost of managing adverse events. Mean cost of managing mild fever per case was RM249, mean cost of managing high fever per case was RM1,036 and mean cost of managing convulsions was RM1,225. Total cost of managing adverse events was RM261 million for mild fever, RM66.7 million for high fever and RM1.3 million for convulsions. Costs of managing mild and high fever were less than the cost of managing convulsions. Total cost of managing mild fever was highest at RM261 million compared with RM66.7 million for high fever and RM1.3 million for convulsions. Thus, lower risk of adverse events actually contributed to higher costs of managing the adverse event.