Abstract: 　Objective　To explore the association between variation in genes related to lipid metabolism and the susceptibility of nonalcoholic fatty liver disease (NAFLD). Methods　Obese children with fatty liver aged 6~18 years old were included. All of them got ultrasonic testing, routine examination and biochemical detection. In addition, the DNA of peripheral blood was extracted and the 36 target genes related to lipid metabolism were detected by next generation sequencing.  Results　In 368  obese children who met the inclusion criteria, 183 children (49.7%) were detected to have NAFL . 100 children with NAFLD and 100 children without NAFLD were randomly selected from obese children. The levels of body mass, waistline, alanine aminotransferase (ALT),  triacylglycerol (TG), cholesterol, low density lipoprotein (LDL) and apolipoprotein B (ApoB) in NAFLD children were all higher than those in non-NAFLD children, and there were significant differences (P all<0.05). However, the levels of aspartate aminotransferase (AST), alkaline phosphatase (ALP), apolipoprotein A1 (ApoA1), fasting blood glucose, insulin, high density lipoprotein (HDL), free fatty acid (FFA) and insulin resistance index (HOMA-IR) were not significantly different between the two groups (P all>0.05). The levels of bilirubine in the two groups were within normal range. Logistic regression analysis showed that the genes of MTTP rs2306986 (OR=2.70, 95%CI: 1.38~5.27) and MTTP rs3792683 (OR=7.34, 95%CI: 2.04~26.50) that encode microsomal triglyceride transfer protein (MTTP or MTP), and the mutation of rs738409 (OR=2.11, 95%CI:1.31~4.48) in gene PNPLA3 that encode patatin-like phospholipase domain-containing protein 3 are the independent risk factors for the occurrence of the disease. Conclusion　Genovariation of MTTP rs2306986, MTTP rs3792683, and PNPLA3 rs738409 may increase susceptibility to NAFLD in children.