Mitochondrial dysfunction, associated with insulin resistance, is characterized by low expression of PGC-1 and nuclear encoded mitochondrial genes. This deficit could be due to decreased physical activity or a decreased response of gene expression to exercise. The objective of this study was to investigate whether a bout of exercise induces the same increase in nuclear encoded mitochondrial gene expression in insulin sensitive and insulin resistant subjects matched for exercise capacity. Seven lean and nine obese subjects took part. Insulin sensitivity was assessed by an 80 mU·m^-2·min^-1 euglycemic clamp. Subjects were matched for aerobic capacity and underwent a single bout of exercise at 70% and 90% of maximum heart rate with muscle biopsies at 30 and 300 min post-exercise. Quantitative RT-PCR and immunoblot analyses were used to determine the effect of exercise on gene expression and protein abundance and phosphorylation. In the post exercise period, lean subjects immediately increased PGC-1 mRNA level (reaching a 8 fold increase by 300 min post exercise), and protein abundance and AMPK phosphorylation. Activation of PGC-1 was followed by increase of NRF-1 and cytochrome c oxidase (subunit VIc). However, in insulin resistant subjects, there was a delayed and reduced response in PGC-1 mRNA and protein, and phosphorylation of AMPK was transient. None of the genes downstream of PGC-1 were increased after exercise in insulin resistance. Insulin resistant subjects have a reduced response of nuclear encoded mitochondrial genes to exercise, and this could contribute to the origin and maintenance of mitochondrial dysfunction.