The incidence of pertussis requiring hospitalization in children younger than 16 years was estimated by the use of an active surveillance-system. Of special interest were differences between West and East Germany following different vaccination strategies before reunification. In 1997 and 1998, 754 pertussis cases required a total of 11,151 hospital inpatient days. The incidence of hospitalized pertussis was 2.68/100,000 person years and this was significantly higher in East than in West Germany. In East Germany an unusually high percentage of hospitalized cases was found in children aged 6-15 years (45% versus 13% in West Germany). The difference between the regions may be due either to a different perception of the disease or to an increased immunity induced by prior disease or vaccination. In East Germany, pertussis was rare until reunification but it has increased significantly since then. Older children may thus represent a population at risk of pertussis having not had previous exposure to pertussis antigens.