To assess whether adolescents with high body mass index (BMI), or fat mass index (FMI), in combination with insulin resistance (assessed with the Homeostatic Model Assessment [HOMA] index), had also lower blood vitamin B6, folate and vitamin B12 concentrations.Six hundred and fifteen adolescents from the Healthy Lifestyle in Europe by Nutrition in Adolescence (HELENA) study, with data on B-vitamins (both intakes and status), and BMI, FMI, HOMA, were selected. Intakes were assessed by two non-consecutive 24-h recalls. B-vitamins biomarkers were measured by chromatography and immunoassay. Analysis of covariance was applied to elucidate the differences in B-vitamins between combinations of groups defined according to the median of the z-scores of markers of body composition and insulin sensitivity.When considering energy intakes and education of the mother in the model, in females, vitamin B6 intakes were higher in the high BMI/high HOMA group than in the high BMI-low HOMA group. Similarly, vitamin B6 intakes were higher in the high FMI/high HOMA group than in the low FMI/low HOMA group. Plasma vitamin B12 was significantly lower in males in the high FMI/high HOMA group than in the low FMI/low HOMA group, keeping also significant their trends throughout the groups, a fact that can be observed also for females (p < 0.05).Adolescents with combined higher adiposity and higher HOMA insulin sensitivity showed lower vitamin B12 plasma concentrations. These differences do not seem to be explained by dietary vitamin B12 intake.