Background: In order to assess the relationship between hypertension or dyslipidemia and obesity, the body mass index (BMI) is usually used. Unlike waist circumference (WC), BMI does not reflect body fat distribution. The aim of this study is to investigate whether BMI or WC is a better predictor of hypertension or dyslipidemia in overweight/obese children and adolescents. Methods: As of November 2012, the APV database contained data on 81,819 patients from 189 specialized pediatric obesity institutions in Germany, Austria and Switzerland. Logistic regression analysis was conducted using odds ratios (OR) with 95% CI. Results: The average age of the youths (n = 5.978) was 13.9 ± 1.8 years. Mean BMI-SDS was 2.0 ± 0.5, and mean WC-SDS was 2.2 ± 0.5. Both BMI-SDS and WC-SDS are significant predictors of hypertension and dyslipidemia: BMI-SDS is a better predictor (OR = 2.60) for hypertension than WC-SDS (OR = 1.85), while WC-SDS (OR = 1.90) was slightly superior to BMI-SDS (OR = 1.86) in predicting adverse lipid profiles. Compared to normal-weight patients, obese patients (BMI ≥97th percentile) exhibited increased systolic (+6.3 mm Hg) and diastolic blood pressure (+3.9 mm Hg). However, this difference was only +4.8 mm Hg (systolic) and +2.6 mm Hg (diastolic) if WC >97th percentile was used. Conclusion: BMI-SDS is more closely associated with hypertension, while WC-SDS is more closely associated with dyslipidemia. However, the additional measurement of WC has only a small benefit in obese youths.