Aims: Choline-deficient diet is extensively used as a model of nonalcoholic fatty liver disease (NAFLD). In this study, we explored genes in the liver for which the expression changed in response to the choline-deficient (CD) diet. Main methods: Male CD-1 mice were divided into two groups and fed a CD diet with or without 0.2% choline bitartrate for one or three weeks. Hepatic levels of choline metabolites were analyzed by using liquid chromatography mass spectrometry and hepatic gene expression profiles were examined by DNA microarray analysis. Key findings: The CD diet lowered liver choline metabolites after one week and exacerbated fatty liver between one and three weeks. We identified >300 genes whose expression was significantly altered in the livers of mice after consumption of this CD diet for one week and showed that liver gene expression profiles could be classified into six distinct groups. This study showed that STAT1 and interferon-regulated genes was up-regulated after the CD diet consumption and that the Statl mRNA level was negatively correlated with liver phosphatidylcholine level. Statl mRNA expression was actually up-regulated in isolated hepatocytes from the mouse liver with the CD diet. Significance: This study provides insight into the genomic effects of the CD diet through the Statl expression, which might be involved in NAFLD development. (C) 2017 Elsevier Inc. All rights reserved.