The present study assessed whether compliance with the Food-Based Dietary Guidelines is related to habitual fatty acid (FA) intake and blood lipid parameters.Dietary information was collected by two non-consecutive 24-h recalls in 1804 European adolescents. Compliance with the Food-Based Dietary Guidelines was expressed by calculating the Diet Quality Index for Adolescents (DQI-A). Blood samples were collected in a randomly selected subset (n = 552). Relations between FA intake/serum concentrations and DQI-A were tested with multilevel regression analysis to correct for the study design (clustering within cities). Analyses were stratified for gender; age was entered as a covariate.Better DQI-A scores were related to increased proportional intakes of energy from total fat, saturated FA, monounsaturated FA, and cholesterol (P < 0.001), whereas no significant association was observed with polyunsaturated FA intakes. In adolescents with higher compared with lower DQI-A scores, dairy products contributed more (21.0% versus 12.7%) and low-nutrient, energy-dense items contributed less (17.2% versus 26.3%) to the intake of total fat. A positive association was observed between the DQI-A scores and serum concentrations of eicosapentaenoic acid and docosahexaenoic acid (all P < 0.005). The latter, however, was significant only in girls. In boys, higher DQI-A scores were inversely associated with serum cholesterol concentrations (P < 0.05).Although compliance with the Food-Based Dietary Guidelines was not always associated with a favorable FA intake pattern, a significant favorable association with some serum biomarkers was observed. This outcome underlines the importance of considering dietary habits instead of single-nutrient intakes.