Flavonoids have been implicated in the prevention of cardiovascular diseases (CVD). In a prospective approach, we investigated whether habitual flavonoid intake from fruit, vegetables and juices (FlavFVJ) during adolescence is associated with adult levels of serum lipids, one of the main CVD risk factors. This analysis included healthy participants from the Dortmund Nutritional and Anthropometric Longitudinally Designed (DONALD) study, who had provided a fasting blood sample in adulthood (aged 18-39 years), data on FlavFVJ intake during adolescence (females: 9-15 years, males: 10-16 years)-estimated either from multiple 3-day weighed dietary records ( = 257), or from validated biomarker hippuric acid (uHA) excretion from multiple 24-h urine samples ( = 233)-together with information on relevant covariates. In multivariable linear regression analyses, a higher FlavFVJ intake during adolescence was independently associated with higher serum high-density lipoprotein cholesterol (HDL-C) levels among males ( = 0.038); however, the inclusion of adult waist circumference attenuated this association ( = 0.053). FlavFVJ was not associated with triglycerides (TG), total cholesterol (TC) or low-density lipoprotein cholesterol (LDL-C; all ≥ 0.1), nor was uHA excretion with any serum lipid outcome among males (all ≥ 0.5). Neither FlavFVJ intake nor uHA excretion was associated with serum lipids among women (all ≥ 0.1). However, a higher flavonoid intake from fruit and vegetables was independently related to lower LDL-C levels ( = 0.021), while a higher intake from juices was associated with higher LDL-C levels ( = 0.016) among females. In conclusion, a higher flavonoid intake from fruit, vegetables and/or juices during adolescence may be linked to cholesterol levels in early adulthood in a sex- and food source-specific manner.