Objective: The purpose of this study was to determine the relationships between the body composition characteristics, body mass index (BMI), sum of skinfolds (SSF), % body fat (%BF), fat-free mass (FFM) and waist-to-hip ratio (WHR), and nine physical fitness items in undernourished rural primary school children in Ellisras, South Africa. Design: A cross-sectional study. Setting: The study consisted of 462 boys and 393 girls who were aged 7-14 y. Measurements: Five body composition measures were assessed: BMI, SSF, %BF, FFM and WHR. Nine physical fitness test items were assessed: standing long jump, bent arm hang, sit-ups, 10 Â 5 m shuttle run, 50 m sprint, 1600 m run, flamingo balance, sit and reach, plate tapping. Results: BMI was highly correlated with FFM (r ¼ 0.7, Po0.001). In line with findings from Western countries, regression coefficients (B) showed that children with higher BMI or SSF performed worse in bent arm hang (girls, B ¼ À0.84, Po0.001, and B ¼ À0.06, P ¼ 0.02, respectively) and in 1600 m run (B ¼ 6.68, Po0.001). BMI was significantly associated with flamingo balance (B ¼ 0.26, P ¼ 0.04). WHR was positively associated with bent arm hang (B ¼ 9.37, P ¼ 0.03), and inversely with sit and reach (B ¼ À7.48, P ¼ 0.01). In contrast, significant relationships were found between BMI and standing long jump (B ¼ 0.74, P ¼ 0.04), sit and reach (B ¼ 0.51, Po0.001), flamingo balance (B ¼ 0.26, P ¼ 0.04) and plate tapping (B ¼ À19, P ¼ 0.01). SSF was significantly associated with sit and reach (B ¼ 0.04, P ¼ 0.03). Significant inverse associations were found between FFM and bent arm hang (girls, B ¼ À0.06, P ¼ 0.05), 1600 m run (girls, B ¼ À2.33, P ¼ 0.003) and 50 m run (boys, B ¼ À0.11, P ¼ 0.006). FFM was significantly associated with standing long jump (boys, B ¼ 0.99, Po0.001; girls, B ¼ 0.73, Po0.001), flamingo balance (B ¼ 0.17, Po0.001), and with sit and reach (boys, B ¼ 0.59, P ¼ 0.03).