The Korean Genome Epidemiology Study (KoGES) is a principal cohort study providing valuable evidence for the prevention of major chronic diseases such as hypertension, obesity, and diabetes in Korea. Since 2001, the Ansan-Anseong cohort is one of the representative cohorts in the KoGES and recruited about 10,000 participants from Ansan and Anseong city to undergo a comprehensive health examination biennially. About 3,000 participants in the Ansan cohort underwent abdominal computed tomography scan to detect the presence of nonalcoholic fatty liver disease (NAFLD). The prevalence of NAFLD was about 23% in this study, and it was twice as high in subjects with diabetes compared to those without. Subjects with NAFLD had early diastolic dysfunction in tissue Doppler study and showed lower vitamin D concentrations than those without. We also found that the palatin-like phospholipase domain containing 3 single nucleotide polymorphisms were significantly associated with NAFLD. Interim prospective analysis after six years showed that NAFLD was associated with worsening of metabolic risk factors and an about 2.6 higher likelihood of developing diabetes than in those without. These results present the clinical importance of the diagnosis and treatment of NAFLD to reduce the future development of diabetes and cardiovascular diseases.