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Background: Many observational studies explore the relationship between homocysteine (Hcy) and nonalcoholic fatty liver disease (NAFLD), whereas the causality of this association remains uncertain, especially in European populations. We performed a bidirectional Mendelian randomisation study to elucidate the causal association between Hcy and NAFLD. Furthermore, we explored the relationship of Hcy with liver enzymes, including alkaline phosphatase (ALP), alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Methods: Two‐sample Mendelian randomisation study was conducted. Summary statistics for Hcy were obtained from a genome‐wide association studies (GWAS) meta‐analysis comprising 44,147 subjects. Summary‐level data for NAFLD were acquired from a GWAS meta‐analysis of 8434 cases and 770,180 noncases and another GWAS meta‐analysis of 1483 cases and 17,781 noncases. Summary‐level data for three liver enzymes were available from the UK Biobank. Results: Genetic associations of Hcy concentrations with NAFLD and liver enzymes were observed. Genetically predicted higher Hcy concentrations were consistently associated with an increased NAFLD risk in two data sources. The combined odds ratio of NAFLD was 1.25 (95% confidence interval [CI], 1.05–1.45) per SD increase in Hcy concentrations. Genetically predicted higher Hcy concentrations showed significant association with ALP (Beta.69; 95% CI, 0.04–1.34), ALT (Beta 0.56; 95% CI, 0.15–0.97) and AST levels (Beta.57; 95% CI, 0.10–1.04). Genetic liability to NAFLD was not associated with Hcy concentrations. Conclusions: This study has clinical implications as it indicates that increased Hcy concentrations increase the relevant liver enzymes and may play a role in NAFLD risk in European populations. [ABSTRACT FROM AUTHOR]