Pertussis is an acute bacterial disease involving the respiratory tract. The causal agent is Bordetella pertussis. Among all age groups, infants (aged < 12 months) have had the highest incidence of pertussis in the vaccine era. The majority of hospitalisations, complications and deaths occurred in that age group. The aim of this study was to describe and characterize the epidemiological pattern of hospitalized pertussis cases during the period of 2000-2006 in the hospitals of Northern Portugal. We conducted a retrospective observational study based on hospitalisations in the Northern region of Portugal between 2000 and 2006. Descriptive summary statistics for all variables were calculated at region, district and municipality levels. The average rates of hospitalisation were calculated per 100,000 population for the region, district and municipality, according to sex and age group. The severity of disease was evaluated on the basis of the average length of hospitalisation, the proportion of patients treated in intensive care units, and the case fatality rate. Three hundred and twenty two cases were identified between 2000 and 2006 in the Northern region of Portugal. Viana do Castelo and Braga districts were those who had the highest hospitalisations rate. In the district of Bragança there were no cases of hospitalisation with the diagnosis of pertussis. Fifty six per cent of the cases were male. The proportion of infants hospitalized under one year was 91.0 %. Cases among infants younger than two months accounted for 43.5 % of all cases. The mean annual hospitalisation incidence rate for infants under one year was 114 per 100,000. The mean length of hospital stay was eight days. The proportion of patients treated in intensive care units was 11.0 %, and case fatality rate was 0.3 %. This hospital-based study indicates that pertussis continues to be an important cause of morbidity and mortality in infants. Pertussis incidence remains high among infants, most of whom are under one year of age. Immunization strategies in the adult population must be reviewed and updated in order to attain higher protection of the more vulnerable paediatric population.