The objective of this study was to investigate the development and tracking of nutritional status, body composition and physical fitness, and the longitudinal relationship of changes in nutritional status, and body composition with changes in physical fitness over a 1-year period of follow-up. Studied were 380 boys and 322 girls aged 7-14 years from the Ellisras Longitudinal Study. Boys and girls were divided into two groups of pre-adolescence (<11 years) and adolescence (>10 years). High tracking coefficients (>8) were found for nutritional status, body mass index, and fat-free mass, while low tracking coefficients (<4) were found for the sum of skinfolds, fat mass, arm muscle area, and central fat distribution. Moderate and low tracking coefficients were found for the physical fitness items. Longitudinal regression analyses showed that physical fitness performances that require a high energy flux over a short period of time are affected by muscle wasting, whereas having a low body weight appears to be important for a good performance on other fitness items in these malnourished rural South African children.