Background There is little information on the effects of diets containing high &#945;-linolenic acid (C18:3n-3) on liver lipid composition and lipogenic gene expressions. In this study fourteen goats (Capra aegagrus hircus) were fed either a flaxseed oil (FSO) supplemented diet containing high &#945;-linolenic acid or a control diet without added flaxseed oil (CON) for 100-d to evaluate the effects on liver lipid composition and the gene expression of peroxisome proliferator-activated receptors (PPAR-&#945;) and stearoyl-CoA-desaturase (SCD) in the liver. Results An increase in the levels of C18:3n-3 and C20:5n-3, C22:5n-3, C22:6n-3 was observed in the liver of FSO-treated goats. There was a significant (P < 0.05) up-regulation of PPAR-&#945; gene expression and downregulation of SCD gene in the liver of goats fed the high &#945;-linolenic acid diet. Conclusions In conclusion, genes associated with the control of fatty acid (FA) conversion (SCD and PPAR) were affected by the &#945;-linolenic acid supplementation in the goat diet. It is suggested that PPAR-&#945; is the key messenger responsible for the translation of nutritional stimuli into changes in hepatic gene expression.