Measured fever often forms the basis for defining clinical malaria episodes in children from endemic areas. We measured body temperature every 3 h from 08:00 to 20:00 in 69 children aged 1-5 years during the malaria season in a rural area of The Gambia. Body temperature varied on average by more than one degree Celsius during the course of a day. Mean temperatures were lowest in the early morning and highest in the afternoon. There was a strong positive association between air temperature and body temperature. In highly endemic areas, researchers who use measured fever to assess clinical malaria episodes in population-based surveys should standardize the time of day at which temperature is assessed.