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BACKGROUND Studies investigating a potential association between hypothyroidism and non-alcoholic fatty liver disease (NAFLD) showed conflicting results and large-scale population-based data from Germany on this topic are currently missing. OBJECTIVE It was the aim of this analysis to investigate the impact of thyroid gland disorders on the prevalence of NAFLD in Germany. METHODS In this case-control study, using the German disease Analyzer database (IQVIA), NAFLD patients were matched to patients without NAFLD by age, sex, index year, treating physician, diabetes mellitus type II, and obesity. The main outcome of the study was an association between thyroid gland disorders (hypothyroidism, hyperthyroidism and autoimmune thyroiditis) and incident NAFLD and was evaluated using logistic regression analyses. RESULTS 57,483 patients with NAFLD were matched to 57,483 patients without liver disease. Mean age of the cohort was 60.3 years (±14.1) and 52.3% were men. In regression analyses, hypothyroidism (OR 1.17, 95% CI 1.10 - 1.24, p < 0.001) as well as autoimmune thyroiditis (OR 1.53, 95% CI 1.35-1.73, p < 0.001) were associated with a higher risk of NAFLD. In contrast, hyperthyroidism was associated with a lower risk of NAFLD (OR 0.85, 95% CI 0.77-0.94, p < 0.001). The effect of hypothyroidism on the prevalence of NAFLD remained significant across men (OR 1.31, 95% CI 1.15-1.48) as well as women (OR 1.12, 95% CI 1.05-1.21). CONCLUSION Hypothyroidism seems to be a risk factor for incident NAFLD.