Participating children with missing data, significantly, more often had a migration background, lower results in the 6 min run test, and they differed in all anthropometric measurements from the ones with complete data. Participants with missing data had significantly higher BMI percentiles, more often were overweight and obese, and more often had a higher waist circumference and a higher WHtR. They also were more often abdominally obese and more often had a percentage of body fat at or above the 95th percentile than their counterparts. Finally, their parents were significantly more often single parents, less frequently had a tertiary educational level and more often a household income at or below €1,750.