Lipid oversupply plays a role in developing insulin resistance in skeletal muscle, decreasing expression of nuclearencoded mitochondrial genes, and increasing extracellular matrix remodeling. To determine if a decrease in plasma lipid content reverses these abnormalities, insulin-resistant subjects with a family history of type 2 diabetes had euglycemic clamps and muscle biopsies before and after acipimox treatment to suppress free fatty acids. Free fatty acids fell from 0.584 ؎ 0.041 to 0.252 ؎ 0.053 mmol/l (P < 0.001) and glucose disposal increased from 5.28 ؎ 0.46 to 6.31 ؎ 0.55 mg ⅐ kg ؊1 ⅐ min ؊1 (P < 0.05) after acipimox; intramuscular fatty acyl CoA decreased from 10.3 ؎ 1.9 to 4.54 ؎ 0.82 pmol/mg muscle (P < 0.01). Paradoxically, expression of PGC-1-and nuclear-encoded mitochondrial genes decreased after acipimox, and expression of collagens I and III ␣-subunits (82-and 21-fold increase, respectively, P < 0.05), connective tissue growth factor (2.5-fold increase, P < 0.001), and transforming growth factor-1 increased (2.95-fold increase, P < 0.05). Therefore, a reduction in lipid supply does not completely reverse the molecular changes associated with lipid oversupply in muscle. Changes in expression of nuclearencoded mitochondrial genes do not always correlate with changes in insulin sensitivity. Diabetes 56:743-752, 2007