Malaria is a major cause of morbidity and mortality in children and adults in the Sudano Sahel of Northeastern Nigeria with the highest prevalence of malaria in pregnancy of 64.5 in Nigeria recorded in this region. This study was carried out in 2003 and 2004 to provide parasitological baseline data for the development of Malaria Early Warning System (MEWS) for the surveillance of type I epidemic caused by meteorological conditions and to provide data for timing malaria key vector control measures such as Indoor Residual Spraying (IRS) for maximum effect. Clinical information about malaria cases were used in this study. In all 692 children aged 6 to 96 months were screened for Plasmodium infection and used for the analysis. The results showed that the majority of infected children (68.06%) were aged 12-60 months and their asexual parasite density (ap/ u1) was between 100-500 ap/u1 of the whole blood. The month of September recorded the highest Geometric Mean Asexual-Densities (GMPD) of 13,655 while the lowest parasite densities were observed at the peak of the dry season, especially during the months of March and April. Significance difference (p<0.05) was observed between the sexes in infection rate. It is obvious that male children have higher infection rate (about 67.5%), than while female children (32.5%) regardless of climate seasonality. Designing a malaria early warning system and providing baseline parasitological data for timing of spraying cycles for key malaria vector control measures such as Indoor Residual Spraying (IRS) should be encouraged to complement other effective malaria control strategies .Hence the need for this investigation.