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Background & Aims: Fatty liver disease (FLD) is common in women with polycystic ovary syndrome (PCOS). Here, we use non‐invasive tests to quantify liver injury in women with PCOS and analyse whether FLD‐associated genetic variants contribute to liver phenotypes in PCOS. Methods: Prospectively, we recruited women with PCOS and controls at two university centres in Germany and Poland. Alcohol abuse was regarded as an exclusion criterion. Genotyping of variants associated with FLD was performed using TaqMan assays. Liver stiffness measurements (LSM), controlled attenuation parameters (CAP) and non‐invasive HSI, FLI, FIB‐4 scores were determined to assess hepatic steatosis and fibrosis. Results: A total of 42 German (age range 18–53 years) and 143 Polish (age range 18–40 years) women with PCOS, as well as 245 German and 289 Polish controls were recruited. In contrast to Polish patients, Germans were older, presented with more severe metabolic profiles and had significantly higher LSM (median 5.9 kPa vs. 3.8 kPa). In the German cohort, carriers of the PNPLA3 p.I148M risk variant had an increased LSM (p =.01). In the Polish cohort, the minor MTARC1 allele was linked with significantly lower serum aminotransferases activities, whereas the HSD17B13 polymorphism was associated with lower concentrations of 17‐OH progesterone, total testosterone, and androstenedione (all p <.05). Conclusions: FLD is common in women with PCOS. Its extent is modulated by both genetic and metabolic risk factors. Genotyping of variants associated with FLD might help to stratify the risk of liver disease progression in women suffering from PCOS. [ABSTRACT FROM AUTHOR]