Agricultural activities, among other factors, can influence the transmission of malaria. In two villages of central Côte d'Ivoire (Tiémélékro and Zatta) with distinctively different agro-ecological characteristics, we assessed Plasmodium prevalence rates, fever and clinically confirmed malaria episodes among children aged 15 years and below by means of repeated cross-sectional surveys. Additionally, presumptive malaria cases were monitored in dispensaries for a 4-year period. In Tiémélékro, we observed a decrease in malaria prevalence rates from 2002 to 2005, which might be partially explained by changes in agricultural activities from subsistence farming to cash crop production. In Zatta, where an irrigated rice perimeter is located in close proximity to human habitations, malaria prevalence rates in 2003 were significantly lower than in 2002 and 2005, which coincided with the interruption of irrigated rice farming in 2003/2004. Although malaria transmission differed by an order of magnitude in the two villages in 2003, there was no statistically significant difference between the proportions of severe malaria episodes (i.e. axillary temperature>37.5 degrees C plus parasitaemia>5000 parasites/microl blood). Our study underscores the complex relationship between malaria transmission, prevalence rate and the dynamics of malaria episodes. A better understanding of local contextual determinants, including the effect of agricultural activities, will help to improve the local epidemiology and control of malaria.