Objective: To investigate the associations between single nucleotide polymorphisms of UDP glucuronosyltransferase Family 1 Member A1 ( UGT1A1 ) with non alcoholic fatty liver disease (NAFLD) and levels of serum lipids in Beijing children, and to provide scientific evidence for the study of genetic mechanism. Methods: In total, 1 027 children aged 7-18 years were recruited from two primary schools and three middle schools from Haidian district of Beijing, who were randomly assigned to case group ( n =162) and control group ( n =865). General condition and medical history were collected by trained field health workers. Height, weight and liver ultrasound were examined. Additionally, fasting venous blood were collected to detect serum total cholesterol (TC), triglyceride (TG), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C) and alanine aminotransferase (ALT). The single nucleotide polymorphisms (SNPs) of UGT1A1 were genotyped. Binary logistic regression and multiple linear regression were applied to analyze the associations between three SNPs of UGT1A1 and NAFLD, ALT and levels of serum lipids. Results: The SNP rs 10929303 (C>T) of UGT1A1 was negatively associated with NAFLD( OR=0.51, 95%CI=0.32- 0.83 , P =0.01), while the SNP rs 4148323 (G>A) was negatively associated with the serum level of TC ( B=-0.10, 95%CI=-0.19- -0.02 , P =0.02); in addition, results were consistent regardless of whether the TC level was measured using a categorical variable or continuous variable. Conclusion The SNP rs 10929303 of UGT1A1 is associated with NAFLD, and the SNP rs 4148323 of UGT1A1 is associated with TC levels in Beijing children.