We prospectively followed 725 children under 2 years of age with laboratory-diagnosed Bordetella pertussis infection to investigate the hospitalization rate and complications. Diagnosis was made by culture and polymerase chain reaction (PCR) from nasopharyngeal swabs in 11,016 children who presented with > or = 7 days of cough at 63 pediatric practices in Germany. Of these children, 33 (4.5%) were hospitalized at a mean age of 4.8 months (range, 17 days to 19.5 months). Complications occurred in 16 (48%) of the 33 patients. Pneumonia developed in two (6%) children and a convulsion was observed in one (3%). Intensive care monitoring was required for 23 (70%) children. Further complications were bradycardia (21%), apnea (12%), conjunctivitis (12%), loss of weight (12%), otitis media (6%), atelectasis (3%) and dehydration (3%). Children aged 6-24 months who had not received any dose of pertussis vaccine had a ten-fold increased risk of hospitalization compared to those who had been partially or fully immunized (p < 0.05). Pertussis immunization should be given at an early point in time and completely in order to prevent severe courses of pertussis and hospitalization in young children.