INTRODUCTION: Pertussis or whooping cough continues to be a major cause of morbidity and mortality in infants younger than 1 year old. OBJECTIVES: To describe the clinical and epidemiological profile of Bordetella pertussis and to analyze the factors associated with confirmation by PCR and case fatality rate. MATERIAL AND METHODS: Prospective, cohort study conducted between December 2003 and December 2011. The study included children seen at the Hospital de Niños Ricardo Gutiérrez suspected of pertussis. The factors associated with confirmation by PCR and the case fatality rate by relative risk (RR) with a 95% confidence interval were studied. RESULTS: Six hundred and twenty patients with a 38% of positive cases (236/620) were included, 3 cases were confirmed by epidemiological link. Confirmed cases (239) showed a seasonal pattern from September through February, a median age of 3 months old, and 89% had received less than three vaccine doses. Eighty six percent of patients were hospitalized: their median length of stay was 7 days. A total of 99% of patients were eu-trophic, 98% were immunocompetent and 17.5% required intensive care. The clinical presentation was analyzed in 480 patients. Of them, 38% (184) had a positive PCR result and their symptoms were: 96.2%, cough; 76.5%, paroxysmal cough; 57.9% cyanosis; 55.7%, respiratory distress; 29%, fever; 22.4%, apnea; 21.9%, vomiting after coughing. A multivariate analysis identified the following as independent predictors associated with confirmation of pertussis by PCR: paroxysmal cough (OR 2.52: 1.50-4.22; p= 0.000) and leukocytosis upon admission >20 000 white blood cells/mm3 (OR 7.96: 4.82-13.17; p= 0.000); having developed fever reduced the chance of having a positive PCR result (OR 0.47: 0.29-0.77; p= 0.003). The case fatality rate for hospitalized patients was 6.8%. Leukocytosis >30 000 white blood cells/mm3 was a predictor of fatality (RR 6.7: 1.88-23.9; p= 0.001). CONCLUSIONS: Confirmed cases were mostly infants younger than 1 year old who were healthy before and who had not completed their primary immunization schedule. Paroxysmal cough and leukocytosis were associated with PCR diagnosis, while leukocytosis was a predictor of mortality.