Whooping cough is currently the worst controlled vaccine-preventable disease in the majority of countries. In order to reduce its morbidity and mortality, it is essential to adapt vaccination programmes to data provided by epidemiological surveillance. A population-based retrospective epidemiological study to estimate the minimum annual undernotification rate of pertussis in Spain from 1997 to 2010 was performed. The incidence of pertussis cases reported to the National Notifiable Disease Surveillance System was compared with the incidence of hospital discharges for pertussis from the National Surveillance System for hospital data, Conjunto Mínimo Básico de Datos. The overall reported incidence and that of hospitalisation for whooping cough were 1.3 cases × 100,000 inhabitants in both cases. Minimum underreporting oscillated between 3.8 and 22.8 %, according to the year of the study. The greatest underreporting (50 %) was observed in children under the age of 1 year. Conclusion: Spanish epidemiological surveillance system of pertussis should be improved with complementary active systems to ascertain the real incidence. Paediatricians and general practitioners should be sensibilized to the importance of notification because this would be essential for adapting the prevention and control measures of this disease.