Alanine aminotransferase (ALT) has been one of the most useful biomarkers reflecting liver damage. Some studies have proposed that serum ALT levels, even those within the conventional normal range, are associated with metabolic syndrome and fatty liver. We examined the correlation between ALT levels and insulin resistance (IR) and ALT cutoff value for high IR status in Korean adolescents. A total of 886 subjects (461 boys and 425 girls) who participated in the 2009–2010 Korea National Health and Nutrition Examination Survey were included in this study. Multivariable adjusted logistic regression analyses were used to examine the odds ratios and 95 % confidence intervals (CIs) of the prevalence of the highest quartile of the homeostasis model assessment of IR (HOMA-IR) according to the ALT quartile. The cutoff value of ALT for the highest HOMA-IR quartile (Q4) were obtained using receiver operating characteristic curve analysis. The mean ALT value increased as the number of metabolic syndrome components increased, but in only boys (p for trend <0.001), while the IR quartile increased in both boys and girls (all p for trends <0.001). The prevalence of IR (Q4) was only increased in ALT (Q4) in boys after the adjustment for age, body mass index, and waist circumference (OR 2.49; 95 % CI 1.05–5.91; p for trend = 0.017). The cutoff values were 17.0 IU/L in boys and 11.0 IU/L in girls. The highest ALT quartile was associated with an increased prevalence of the highest quartile of IR in boys but not in girls.