From August 2004 to January 2005 a cluster of 7 cases of serogroup B meningococcal disease occurred in the state of Saxony-Anhalt in the town of Sangerhausen and the surrounding area. This led to an investigation of meningococcal carriage in 816 high school students (grades 9 to 13). The students were also asked to fill out a questionnaire regarding possible risk factors for carriage. The goal of the study was the evaluation of a possibly persistently increased risk for further cases in the region. Results of the study were to be used for a comprehensive and targeted education of the public. The percentage of students found harbouring N. meningitidis in the nasopharynx in Sangerhausen (9.0 %) was not elevated compared to that found in the two control regions of Kelbra, County of Sangerhausen (8.2 %) and Jessen, County of Wittenberg (9.9 %). The serogroup B fine type responsible for the cluster (P1.7-2,16:F3-3:PorB3-24) was found only in one student each in Sangerhausen and Kelbra. Thus, there was no evidence of an increased risk for further cases at the time of the study at the end of January, 2005. This may have been due to intensive contact tracing and provision of chemoprophylaxis in Sangerhausen. Visiting a disco or bar and smoking were identified as risk factors for meningococcal carriage. However, these factors were associated with carriage only in boys but not in girls. This may be explained by sex-specific differences in physical interaction with others. Efforts to prevent further cases during clusters of meningococcal disease should consider sex-specific risk behaviour.