Accurate estimates of total daily energy expenditure (TDEE) are critical to studies of the nutritional adaptation of human populations. This study compared the standard factorial method with the recently developed flex-HR technique in a sample of 32 adults (16 males, 16 females) from rural, agricultural communities of highland and coastal Ecuador. Although energy expenditures obtained from the two methods were highly correlated (r = 0.759, P < 0.0001), the 1985 FAO/WHO/UNU factorial method significantly underestimated TDEE relative to the heart rate-monitoring technique (10.27 ± 2.54 compared with 11.91 ± 3.96 MJ/d, P < 0.001). The degree of underestimation was greater in males, who had higher energy expenditures. Similarly, underestimation was greater in the highland farmers, who were studied during a period of heavy agricultural work. The differences in energy expenditure estimates translated into a 10% difference in estimated energy adequacy. Additional research is needed to identify the potential sources of bias in the factorial method and to further develop other techniques for accurately estimating energy expenditure under field conditions.