Meningococcal disease is a major public health concern in Sahelian Africa, where over half of the cases reported worldwide occur. In an effort to find annual spatial clusters of meningococcal disease and in order to study their evolution in Niger from January 2002 to June 2008, a prospective study of routine national surveillance data was conducted pertaining to patients with suspected bacterial meningitis. The diagnoses were obtained by analysing patients' cerebrospinal fluid, using polymerase chain reaction or bacteriology. SatScan using Poisson's model was used to calculate the relative risk (RR) of occurrence of spatial clusters. In the 2002-2003 period, 15 spatial clusters of meningococcal meningitis were detected in a total of 3,979 cases with a maximum number of 558 cases per cluster in the south-eastern part of the country (70.5% of all cases that year; RR = 7.85; P < 0.001). Other clusters were found in the following years in approximately the same area as those detected in 2002-2003. These clusters were identified in the southeast, which allowed us to identify high-risk groups in this part of the country. Statistically significant spatio-temporal patterns were found, which should be useful in establishing hypotheses for prospective studies on epidemic tendencies and empirical risk factors in the African meningitis belt.