It has been suggested that periodontitis is associated with metabolic abnormalities including non-alcoholic fatty liver disease (NAFLD). The fatty liver index (FLI) is a non-invasive surrogate marker and predictor of NAFLD. We aimed to determine whether FLI itself would be associated with periodontitis through a secondary analysis of previously reported nationally representative probability sample data of the Korean population. FLI was calculated from a previously developed algorithm which combines measures of body mass index (BMI), waist circumference, triglyceride, and gamma-glutamyl transferase (GGT). Periodontitis was diagnosed based on the Community Periodontal Index (CPI) developed by the World Health Organization. Of 4,272 participants, 26.1% were diagnosed with periodontitis. Higher FLI was associated with a higher prevalence of periodontitis (Odds ratio (OR) highest vs. lowest quartile of FLI,1.63; 95% confidence interval (CI), 1.23-2.16; P = 0.001 for trend) adjusting for confounding factors. In the highest FLI quartile, prevalence of periodontitis was higher in individuals with diabetes (OR highest vs. lowest quartile of FLI, 2.89; 95% CI, 1.01-8.27 for diabetic subgroup; OR highest vs. lowest quartile of FLI, 1.45; 95% CI, 1.07-1.96 for non-diabetic subgroup). In summary, FLI was associated with prevalent periodontitis.