BMI, skinfold thickness, and circumferential measures were assessed in groups of normal healthy Czech boys (n = 1764) and girls (n = 1762) 3–6 years of age in the late 1950s and 1960s (sample C), in the 1990s (sample B), and in 2014–2016 (sample A). During these decades BMI has not changed significantly, and in selected groups (boys 3, 5, and 6, girls 3 and 6 years) it was most recently found to be significantly lower (P ≤ 0.05). Subscapular, suprailiac, triceps, midthigh, and above patella skinfold thicknesses significantly increased in sample A as compared to sample C (P ≤ 0.001). Comparison of the same skinfolds measured in the nineties (sample B) and more recently (sample A) showed similar increase of subcutaneous fat (P ≤ 0.001). The increase of adiposity characterized by skinfolds occurring in spite of not markedly changed BMI indicates significant changes of body composition—latent (also hidden) obesity. The increase of adiposity was relatively greatest on the trunk (P ≤ 0.001)—which is considered a marker of the greatest health risk. The decrease of femoral circumference (P ≤ 0.05) along with simultaneous increase of thigh skinfold (P ≤ 0.01) revealed the decrease of muscle mass in the lower extremity, obviously due to the reduction of weight-transferring physical activity.