To study the relationship between body fat percent (BF%) and body mass index (BMI) in two different Indonesian ethnic groups (Malays and Chinese) and to relate differences in the relationship to differences in body build and slenderness. Cross-sectional study. Except for ethnicity, not specially selected populations living on Java (Depok, south of Jakarta: Malay Indonesians, n = 117) and on Sulawesi (Makale, north of Ujung Pandang: Chinese Indonesians, n = 109). Weight, height, sitting height, waist and hip circumferences and skeletal widths were measured. BMI was calculated and BF% was predicted from BMI, age and sex using a (Dutch) Caucasian prediction formula. Slenderness was expressed as the ratio of weight: sum of knee and wrist width. BF% assessed by deuterium oxide dilution was used as a reference. BF% in the male and female Malay Indonesians was 24.6+/-7.0 and 35.6+/-5.6% respectively which was not significantly different from the values in the male and female Chinese Indonesians (24.0+/-4.3 and 33.8+/-6.9%). BMI and age were significantly lower in the Malay Indonesians. Malay Indonesians had a more slender body build in terms of skeletal widths compared to the Chinese Indonesians, and they had a higher slenderness index. BF% predicted from BMI using a Caucasian prediction formula was underestimated by 5.8+/-4.8% and 7.7+/-3.8% in the male and female Malay Indonesians but only by 1.3+/-3.0% and 1.7+/-3.7% in the male and female Chinese Indonesians. After correction for differences in age, sex and BF% the Malay Indonesians had a 1.7+/-0.3 kg/m2 (P < 0.0001) lower BMI than the Chinese Indonesians. After correcting for body build and relative sitting height the difference lowered to 0.9+/-0.4 kg/m2 (P < 0.02). The study confirmed the results of an earlier study that Indonesians have a higher BF% at the same BMI compared to Caucasians, but that there are apparently also differences among Indonesian subgroups. These differences are at least partly related to differences in body build.