In areas of highly seasonal Plasmodium falciparum transmission, the presence of a large reservoir of persistently infected but asymptomatic individuals in the dry season leads to predictable increases in the incidence of clinical malaria in the rainy season. Highland areas, by contrast, are prone to unpredictable epidemics of malaria. To determine the importance of persistent asymptomatic infection in highland areas, we assessed asymptomatic individuals in the highland area of Kipsamoite, Kenya for the presence of P. falciparum blood-stage infection by microscopy and PCR. Five sample collections were performed during rainy and dry seasons over a 31-month period. The final collection was obtained at the start of a rainy season epidemic. Asymptomatic parasitemia was infrequent, ranging from 1.3 to 8.1% by microscopy and 5.9 to 14.5% by PCR testing. Microscopy had low sensitivity (22.2-54.8%) but excellent specificity (95.4-100%) in comparison to PCR testing. Frequency of asymptomatic parasitemia did not differ by age. Gametocyte prevalence was <1% in all periods, except at the start of the epidemic, when it increased to 5.3%. In this epidemic-prone highland area, inter-epidemic periods are characterized by low frequencies of asymptomatically infected individuals. Increases in gametocyte prevalence may be an early indicator of impending outbreaks.