This study investigated the effects of dietary conjugated linoleic acid (CLA), in the form of free fatty acid (FFA-CLA) or triacylglycerol (TG-CLA), on serum and liver lipid composition and gene expression associated with lipogenesis and β-oxidation in high-fat-diet (HFD)-induced obese C57BL/6J mice. Animals were fed a control diet, HFD, HFD supplemented with 2% FFA-CLA, or HFD supplemented with 2% TG-CLA for 8 weeks. Supplementation with both forms of CLA significantly reduced the weights of whole body and adipose tissue and was positively associated with significant liver enlargement. Both forms of CLA significantly decreased serum TG concentration, but had no effect on total cholesterol levels, which were increased in mice fed HFD. There was a prominent increase in serum alanine aminotransferase (ALT) levels in mice that received either form of CLA. TG accumulation and lipogenic gene expression, including the expression of genes for fatty acid synthase (FAS), acetyl-coenzyme A carboxylase (ACC), and malic enzyme, were significantly lower in the livers of mice that received TG-CLA as compared to FFA-CLA. The gene expressions of sterol regulatory element binding protein-1c (SREBP-1c) in both liver and adipose tissue were suppressed in mice that were fed either form of CLA as compared to the mice fed HFD alone, whereas there were no increases in the levels of expression of β-oxidation-related genes. These findings demonstrated that free and esterified forms of CLA have differing effects on liver and adipose tissue lipogenesis.