Diagnosis of malaria using only clinical means leads to overdiagnosis. This has implications due to safety concerns and the recent introduction of more expensive drugs. Temperature is a major climatic factor influencing the transmission dynamics of malaria. This study looked at trends in malaria morbidity in the low risk Kenyan district of Nyandarua, coupled with data on temperature and precipitation for the years 2003-2006. July had the highest number of cases (12.2% of all cases) followed by August (10.2% of all cases). July and August also had the lowest mean maximum temperatures, 20.1 and 20.2 degrees C respectively. April, July and August had the highest rainfall, with daily means of 4.0, 4.3 and 4.9 mm, respectively. Observation showed that the coldest months experienced the highest number of cases of malaria. Despite the high rainfall, transmission of malaria tends to be limited by low temperatures due to the long duration required for sporogony, with fewer vectors surviving. These cold months also tend to have the highest number of cases of respiratory infections. There is a possibility that some of these were misdiagnosed as malaria based on the fact that only a small proportion of malaria cases were diagnosed using microscopy or rapid diagnostic tests. We conclude that overdiagnosis may be prevalent in this district and there may be a need to design an intervention to minimise it.