The central highlands in Madagascar are characterized by an unstable occurrence of malaria with the risk of sporadic outbreaks. In major parts of the region DDT indoor spraying campaigns have been carried out from 1993 to 1998. This strategy was in 1999 replaced by another anti-vector intervention program targeting residual foci as detected by a surveillance and early warning system. This system is based on monitoring of presumptive malaria cases in the communities by which the number of presumptive cases exceeded a defined warning threshold value per month. The system was in the follow-up period shown to be very sensitive to variation of the coverage of anti-vector interventions: the number of presumptive cases decreased in the villages in which indoor spraying had been carried out and a minor increase was observed in those villages, where indoor spraying has been suspended. An increase of malaria cases was observed in 44 (20.8%) out of 212 study sites in the same period. The increase was in particular predominant in areas at lower attitude at the outer zones of the central highlands.