Seven repeated cross-sectional parasitological surveys, collecting a total of 13,912 blood samples, were carried out from September 1995 to February 1998 in three irrigated rice growing villages and three villages without irrigated agriculture in the area surrounding Niono, Mali. Parasite prevalence varied according to season and agricultural zone, but showed similar patterns for villages within the same zone. Overall, malaria prevalence was 47% in the villages without irrigated agriculture and 34% in the irrigated rice growing villages. In a village in the irrigated zone, and a village in the non-irrigated zone, 1067 and 608 children up to the age of 14 years, respectively, were followed in a passive malariological study for the period of 13 months. Fevers were attributed to malaria using a statistical method, taking into account the parasitaemia in afebrile controls from the cross-sectional surveys. The incidence of malaria fevers differed markedly between the two zones and over time. In the village in the irrigated zone, the incidence of malaria fevers was fairly constant over the year at 0.7 per 1000 children per day. In the village without irrigated agriculture, incidence was low during the dry season (at 0.6 per 1000 children per day), whereas it was high during the rainy season (at 3.2 per 1000 children per day). These results correspond well to the malaria transmission observed in a concurrent entomological survey. Rice cultivation in the semi-arid sub-Saharan environment altered the transmission pattern from seasonal to perennial, but reduced annual incidence more than two-fold.