Abstract Background Prevalence of Non-Alcoholic Fatty Liver Disease (NAFLD) is increasing in patients with Inflammatory Bowel Disease (IBD), particularly Crohn's Disease (CD). Despite this, the mechanisms and risk factors of NAFLD in IBD are still poorly understood and controversial. The aim of this study was to assess the prevalence and risk factors for NAFLD in patients with CD. Methods Prospective study conducted among consecutive patients with CD and treated at the Inflammatory Bowel Diseases outpatient clinic at University Hospital between July 2021 and May 2022. Demographic, anthropometric and CD characteristics, food intake, previous and current medications, pre-existing diseases, laboratory tests, plasma levels of trimethylamine oxide (TMAO) data were collected. All participants underwent ultrasound (US) of the upper abdomen for evaluation and classification of NAFLD. Results One hudndred and three patients with a mean age of 45.2 ± 15.0 years, 35.9% (n=37) were male. The prevalence of NAFLD was 40.8% (n=42) and overweight (BMI>25kg/m²) was present in 62.1%. Other associated diseases were present among NAFLD patients: systemic arterial hypertension (SAH) 4.9% (p<0,001), dyslipidemia 11.9% (p=0,040) and diabetes (DM) 19% (p=0,009). There were no statistically significant differences between CD characteristics or activity, previous or current CD treatment and food consumption with NAFLD. The presence of comorbidities such as SAH, DM and dyslipidemia, anthropometric markers such as Body Mass Index (BMI), waist circumference (AC), sagittal abdominal diameter (SAD), laboratory tests such as C-reactive protein (CRP), triglycerides (TG) and Liver enzymes were positively associated with the diagnosis of NAFLD. Plasma levels of TMAO showed no significant association with the presence of NAFLD and with CD activity but correlated with SAD (p 0,047). After adjusting for the multivariate model, only the variables SAH (p 0,046), DM (p 0,017), active CD (p 0,023), overweight (p 0,025) and obesity (p<0,001) remained associated to the presence of NAFLD. Conclusion The prevalence of NAFLD in patients with CD was 40.8%, higher than the global prevalence. The main risk factors for NAFLD in this population were like those in the general population such as systemic arterial hypertension, diabetes, dyslipidemia, visceral fat by sagittal abdominal diameter, overweight and obesity. The characteristics of CD, nutrient intake, and plasma levels of TMAO showed no relation with the presence of NAFLD. Crohn's disease activity by IHB and PCR showed a positive correlation with NAFLD. The high prevalence of NAFLD among CD patients should raise this concern for patient care.