Neisseria meningitidis is an important cause of childhood meningitis and septicaemia. Between 1999 and 2005, 133 invasive meningococcal disease (IMD) cases occurred in Jerusalem, 112 (84.2%) of them in children aged 0-14 years. The annual incidence rate in Jerusalem was higher than the national average (2.45+/-0.6 vs. 1.13+/-0.16/100 000 population, P=0.002). Most of the children (82.1%) were from low socio-economic Arab and Jewish ultra-orthodox communities; mortality was higher among Arab than Jewish children (1.3 vs. 0.22/100 000 person-years, P=0.004). A cluster of 10 children with severe meningococcal sepsis (three fatalities) emerged in the winter of 2003-2004. Compared to the other 102 cases in 1999-2005 both meningococcaemia (100% vs. 51%, P=0.003) and mortality (30% vs. 6.9%, P=0.014) rates were higher. Serogroup B comprised 77.6% of the bacterial isolates. Pulsed-field gel electrophoresis showed considerable variability among cluster isolates, but significant resemblance in Arab cases throughout 1999-2005. The increased susceptibility of specific sub-populations to IMD necessitates further evaluation.