Background/Aims: Metabolic syndrome (MS) and fatty liver disease (FLD) are on the rise. The association between these conditions in Brazilian youth is analyzed. Methods: 354 subjects (11.2 ± 3.1 years) were evaluated. FLD was suspected by ultrasound and computed tomography; weight and MS by BMI z-score and NCEP-ATPIII respectively. Results: Subjects were classified as: group 1 with suspected FLD and group 2 without and group 2 as ‘a’ (overweight/obese) and ‘b’ (normal weight). Comparing group 1 with 2a and 2b, differences in age (p = 0.016; p = 0.075), triglycerides (TG) (p = 0.021; p = 0.002), insulin (p = 0.652; p = 0.015) and homeostasis model assessment method of IR (HOMA-IR) (p = 0.737; p = 0.003) were found. Group 2a was divided into low/high alanine aminotransferase (ALT). A decrease in waist circumference and TG was found going from those with suspicion of FLD to obese with high and low ALT. Insulin and HOMA-IR in group 1 and high ALT were similar. Gender (OR 6.6; CI 1.9–22.5; p = 0.025), age (OR 1.3; CI 1.1–1.6; p = 0.006), TG (OR 10.4; CI 3.1–34.4; p = 0.005) were associated with suspected FLD. For every 10 U/l increase in ALT, there was a 4-fold greater chance of probable FLD (OR 4.01; CI 2.06–9.40; p < 0.001). Conclusion: Measurements of ALT and TG should be considered as screening for suspected FLD in overweight/obese youth.