There is a growing consensus that changes in climate will have major consequences for human health through a reduction in the availability of food and an increasing frequency of natural disasters. However, the contribution of higher temperatures to vector-borne diseases, particularly malaria, remains controversial despite the known biological dependence of both vector and pathogen on climate. Misconceptions and inappropriate use of variables and methods have contributed to the controversy. At present there appears to be more support for non-climatic explanations to account for the resurgence of malaria in the African highlands, e.g. the deterioration of malaria control and the development of drug resistance. An attempt is made here to show that dismissing temperature as a driving force in the case of malaria is premature. Using a de-trended time-series of malaria incidence in Madagascar between 1972 and 1989 indicated that a minimum temperature during 2 months at the start of the transmission season can account for most of the variability between years (r2 = 0.66). These months correspond with the months when the human-vector (Anopheles gambiae sensu lato) contact is greatest. The relationship between El Niño Southern Oscillation (ENSO) and temperature (r = 0.79), and ENSO and malaria (r = 0.64), suggests that there might be an increased epidemic risk during post-Niño years in the Madagascar highlands and therefore warrants increased vigilance and extended control efforts in the first half of 2003. This review suggests that the rejection of climate-disease associations in studies so far published may not have used biologically relevant climate parameters. It highlights the importance of identifying more relevant parameters during critical periods of the transmission season in order to aid epidemic forecasting and to assess the potential impact of global warming.