This study compares the role and performance of active case detection (ACD) and passive case detection (PCD) in Jepara district, Indonesia. The number of blood slides examined and positive for malaria reported from 1994-1998 was retrieved from the district surveillance registers. Age of cases, parasite species, types of drugs and dosage, and time lapse were recorded from malaria registers at the three most endemic health centres. The quality of diagnosis was examined by re-reading 153 slides at the Department of Parasitology, Faculty of Medicine, Gadjah Mada University. Almost 60% of the 10,493 confirmed cases in Jepara district were identified from ACD. ACD detected significantly higher P. falciparum gametocyte infections than PCD (14.7% vs. 5.7%; p=0.002). The duration for slides prepared for examination was longer in ACD than in PCD (2.3 vs. 1.1 days; p<0.001), but this was still within the presumptive treatment period. Based on this we conclude that in the transition period to a decentralised health system, ACD for malaria parasites should be continued in a specified endemic area and therefore, efforts to retain the village malaria workers should be considered.