Previously we showed that feeding micropigs ethanol with a folate deficient diet promoted the development of hepatic injury while increasing hepatic levels of homocysteine and S-adenosylhomocysteine (SAH) and reducing the level of S-adenosylmethionine (SAM) and the SAM to SAH ratio. Our present goals were to evaluate mechanisms for hepatic injury using liver specimens from the same micropigs. The effects of ethanol feeding or folate deficient diets singly or in combination on CYP2E1 and signal pathways for apoptosis and steatosis were analyzed using microarray, real-time PCR and immunoblotting techniques. Apoptosis was increased maximally by the combination of ethanol feeding and folate deficiency and was correlated positively to liver homocysteine and SAH. Liver CYP2E1 and the ER stress signals glucose-regulated protein 78 (GRP78), caspase 12, and sterol regulatory element binding protein 1-c (SREBP-1c) were each activated in pigs fed folate deficient or ethanol diets singly or in combination. Liver mRNA levels of CYP2E1, GRP78, and SREBP 1-c, and protein levels of CYP2E1, GRP78, nSREBP, and activated caspase 12 each correlated positively to liver levels of SAH and/or homocysteine and negatively to the SAM to SAH ratio. The transcripts of lipogenic enzymes fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC) and stearoyl-CoA desaturase (SCD) were elevated in the ethanol-fed groups, and each was positively correlated to liver homocysteine levels. The induction of abnormal hepatic methionine metabolism through the combination of ethanol feeding with folate deficiency is associated with the activation of CYP2E1 and enhances ER stress signals that promote steatosis and apoptosis.