Accurate malaria diagnosis has dual roles in identification of symptomatic persons for effective malaria treatment and also enumeration of asymptomatic persons who contribute to the epidemiologic determinants of transmission. Three currently used diagnostic tests, microscopy, rapid diagnostic tests (RDTs), and real-time PCR, all have different sensitivities and specificities, which are parasite density dependent. Here, we compare their concordance among 451 febrile episodes in a cohort of 2,058 children and adults followed over 6 months in a region in central Tanzania with hypoendemic malaria. Microscopy, a histidine-rich protein-based RDT, and two different real-time PCR gene probes detected Plasmodium falciparum in 20, 54, 41, and 78 episodes of fever, respectively. They had complete concordance in only 9 episodes. Real-time PCR with an 18S probe was more sensitive than with a mitochondrial probe for cytochrome b despite higher copy numbers of mitochondrial DNA. Both PCR yields were increased 4-fold by glycogen/acetate precipitation with low-speed centrifugation. Duplicate PCR increases low-density malaria detection. RDT had the highest number of unique positives, presumably from persistent antigen despite the absence of parasites, although RDT did not detect 3 parasitemias with over 1,000 parasites/l. In a latent class analysis, real-time PCR had significantly higher sensitivity than did microscopy or RDT. Agreement between real-time PCR, RDT, and microscopy was highest in March and April, when both the P. falciparum parasite rate and parasite densities are highest. Real-time PCR is more sensitive and specific than RDT and microscopy in low-prevalence, low-parasite-density settings.Low-prevalence, or hypoendemic, malaria poses particular diagnostic challenges because low population prevalence reduces the positive predictive value of tests. Moreover, test sensitivity suffers when parasite densities within individual infections are low (3). The proportion of low-density infections may rise with decreasing transmission (2), so hypoendemicity diminishes test sensitivity, as well as the positive predictive value (3). Malaria diagnostics, such as real-time PCR (RT-PCR), chromatographic rapid diagnostic tests (RDTs), and traditional Giemsa staining and microscopy, have performed differently across ecoepidemiological settings, leading to varying estimates of agreement between tests. Agreement between microscopy and PCR has been shown to be poor under hypoendemicity (malaria prevalence of less than 10%) (5), and agreement between RDT and RT-PCR or microscopy may also decline when the prevalence is low.We compared the yields of RT-PCR, RDT, and microscopy for the diagnosis of Plasmodium falciparum malaria in a cohort of 2,058 adults and children from a district in central Tanzania with hypoendemic malaria followed from January to June 2009. The district has seasonal malaria, coinciding with the rainy season, and in the study year, malaria was hypoendemic. The cohort was assembled to investigate the ancillary benefits o...