In many countries, acellular pertussis vaccines have replaced whole-cell vaccines. We evaluated the impact of a pertussis toxoid vaccine on pertussis in Denmark. We calculated incidence rates for pertussis before and after pertussis toxoid vaccine was introduced, and estimated vaccination effectiveness (VE). We found that routine vaccination with pertussis toxoid vaccine was effective against both hospitalisation with pertussis (VE, 93% for three doses) and non-hospitalised pertussis (VE, 78% for three doses). However, after the introduction we found an increase in pertussis among the youngest infants, a direct result of the new schedule (ages 3, 5 and 12 months) where the youngest infants are unvaccinated for a longer time-period compared with the prior schedule (ages 5, 9 weeks and 10 months).