Background: WHO documents characterize stunting as, “…impaired growth and development that children experience from poor nutrition, repeated infection, and inadequate psychosocial stimulation.” The equation of stunting with malnutrition is common. This contrasts with historic and modern observations indicating that growth in height is largely independent of the extent and nature of the diet. Subjects: We measured 1716 Indonesian children, aged 6.0–13.2 years, from urban Kupang/West-Timor and rural Soe/West-Timor, urban Ubud/Bali, and rural Marbau/North Sumatra. We clinically assessed signs of malnutrition and skin infections. Results: There was no relevant correlation between nutritional status (indicated by skinfold thickness) and height SDS (hSDS). In total 53% of boys, and 46% girls in rural Soe were stunted, with no meaningful association between mean of triceps and subscapular skinfolds (x̅SF) and height. Skinfold thickness was close to German values. Shortest and tallest children did not differ relevantly in skinfold thickness. The same applied for the association between hSDS and mid-upper-arm circumference (MUAC) using linear mixed effects models with both fixed and random effects. In total 35.6% boys and 29.2% girls in urban Ubud were overweight; 21.4% boys and 12.4% girls obese, but with mean hSDS = −0.3, still short. Relevant associations between hSDS and x̅SF and MUAC were only found among the overweight urban children confirming that growth is accelerated in overweight and obese children. There were no visible clinical signs of malnutrition or chronic infection in the stunted children. Conclusion: The present data seriously question the concept of stunting as prima facie evidence of malnutrition and chronic infection.