Elevated alanine aminotransferase (ALT) and non-alcoholic fatty liver disease (NAFLD) have been associated with insulin resistance (IR). The objective of this study was to determine whether elevated ALT and NAFLD were useful for early and definitive determination of IR and to compare their coexistence with conventional risk factors in young Han males. Anthropometric and metabolic measurements were assessed in 216 young Han males (19.3 ± 0.8 years). NAFLD was diagnosed using ultrasonography, and the homeostasis model assessment of insulin resistance (HOMA-IR) served as an index of IR. Subjects in the fourth HOMA-IR quartile had a significantly higher frequency of abdominal obesity, elevated blood pressure and ALT, and NAFLD compared to subjects in quartiles 1–3 (P < 0.05). Using multivariate logistic regression analysis, risk of IR increased by 2.33-fold (95% CI: 1.00–5.42, P = 0.050) in participants with NAFLD. In addition, the coexistence of NAFLD and elevated ALT were significantly associated with HOMA-IR and participants with both elevated ALT and NAFLD had a 4.65-fold (95% CI: 1.55–13.97, P = 0.006) increased risk of IR. Coexistence of NAFLD and elevated ALT are associated with IR in young Han males and might be useful for early detection of IR as compared to conventional risk factors.