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We assessed the nutritional status of 90 pygmies (Efe) and 211 members of a neighboring horticultural Lese in the Ituri forest in northeast Zaire. Clinical signs of iron and iodine deficiency were highly prevalent, but the frequency of these and other clinical signs of nutritional deficiency did not differ between the two groups. Infectious diseases such as yaws, cellulitis, and filiariasis were common. Absolute heights and weights of both Efe males and females aged 2-18 years were less than the 5th percentile of the National Center for Health Statistics standards. Weights for height of both groups were within the normal range. Weights and heights, expressed as percentages of the 50th percentile for age and sex, were significantly lower (P less than .001) in Efe males and females than among Lese males and females, but weights for height did not differ significantly. Z-Scores of height and weight were also significantly lower in Efe males and females than among their Lese counterparts. The differences in weight and height, expressed either as a percentage of the 50th percentile or as Z-scores, were most apparent in older adolescents and persisted among adults. The normal weight for height among both populations indicated that acute undernutrition did not exist at the time of the survey. Despite comparable levels of adult fatness, measured by triceps skinfold thickness, heights of Efe males and females were lower than those of the Lese. These observations support the hypothesis that genetic differences account for the short stature of the Ituri pygmy. However, because the environments shared by the two groups are not identical and because other practices differ, nutritional effects cannot be excluded.