Purpose The role of polyphenol intake during adolescence to prevent metabolic syndrome (MetS) is little explored. This study aimed to evaluate the association between intake of total polyphenols, polyphenol classes and the 10 most consumed individual polyphenols with MetS risk in European adolescents. Methods Of the cross-sectional HELENA study, 657 adolescents (54% girls; 14.8% overweight; 12.5-17.5 year) had a fasting blood sample and polyphenol intake data from two non-consecutive 24-h recalls matched with the Phenol-Explorer database. MetS was defined via the pediatric American Heart Association definition. Multilevel linear regressions examined the associations of polyphenol quartiles with MetS components, while logistic regression examined the associations with MetS risk. Results After adjusting for all potential confounders (socio-demographics and nine nutrients), total polyphenol intake, polyphenol classes and individual polyphenols were not associated with MetS risk. From all MetS components, only BMI z-score was modestly inversely associated with total polyphenol intake. Further sub analyses on polyphenol classes revealed that flavonoid intake was significantly associated with higher diastolic blood pressure and lower BMI, and phenolic acid intake was associated with higher low-density cholesterol. For individual polyphenols, the above BMI findings were often confirmed (not independent from dietary intake) and a few associations were found with insulin resistance. Conclusion Higher intakes of total polyphenols and flavonoids were inversely associated with BMI. No consistent associations were found for other MetS components.