Objective: To examine the associations of insulin resistance at childhood with adiposity changes over a 6-year period (from 9 to 15 years) in a sample of 659 Swedish and Estonian children (52.7% girls) participating in the European Youth Heart Study. Research, Design and Methods: We measured weight, height, waist circumference, biceps, triceps, subscapular, suprailiac, and medial calf skinfolds, and we calculated body mass index (BMI), sum of five skinfolds, and body fat percentage. Fasting plasma glucose and insulin were measured and homeostasis model assessment of insulin resistance (HOMA-IR) was calculated. Changes in puberty stage, sex, centre and the corresponding baseline adiposity values were used as confounders in all analysis. Results: HOMA-IR at childhood was significantly and positively associated with changes in BMI (b ¼ 0.265; P ¼ 0.024), sum of five skinfolds (b ¼ 0.3445; P ¼ 0.003), body fat percentage (b ¼ 1.042; P ¼ 0.016) and waist circumference (b ¼ 0.806; P ¼ 0.002) from childhood to adolescence. These relationships persisted when overweight children were excluded from the analysis. BMI, sum of five skinfolds, body fat percentage and waist circumference at childhood were not significantly associated with changes in HOMA-IR (P for all 40.1). Conclusions: These results give further support to the concept that lower insulin sensitivity at childhood may predict subsequent total and central adiposity gain at adolescence. These findings enhance the role of insulin sensitivity as a target of obesity prevention already from the first decades of life.