In a cross-sectional study design, we test the hypothesis whether childhood obesity is associated with reduced flow rate of stimulated whole saliva and dental caries. Obese adolescents (n = 65) with a mean age of 14.5 years and normal weight subjects (n = 65) with a mean age of 14.2 years were clinically examined with respect to dental caries, visible plaque accumulation (visible plaque index (VPI%)), gingival inflammation in terms of bleeding on probing (BOP%) as well as answered a questionnaire concerning medical history, medication, oral hygiene habits, smoking habits, and sociodemographic background. The flow rate of stimulated whole saliva (ml/min) was determined. BMI was calculated and adjusted for age and gender (BMI-sds). The obese subjects exhibited higher number of decayed surfaces (DS), 0.7 vs. 0.1 (P = 0.008) and lower flow rate of stimulated whole saliva 1.2 vs. 2.0 ml/min (P < 0.001). Of obese patients, 17 subjects had VPI% >25 and 21 had BOP% >25, both compared to only 5 subjects of the normal weight with P values of 0.005 and <0.001, respectively. In a multivariate logistic regression model BMI-sds was significantly associated with the flow rate of stimulated whole saliva less than the median value 1.5 ml/min (P < 0.001; odds ratio (OR) 1.36) as well as with DS (DS >0) (P = 0.002; OR 1.31) and the associations were not found to be confounded by any of the studied variables. The results indicate that childhood obesity is associated with reduced flow rate of stimulated whole saliva and dental caries and further strengthens obesity's negative effect on children's oral health.