Peroxisome proliferator activated receptor-alpha (PPAR) is a key regulator of fatty acid oxidation in skeletal muscle but few data exist from humans in vivo. To investigate whether insulin sensitivity in skeletal muscle and BMI were associated with skeletal muscle expression of PPAR and with important genes regulating lipid metabolism in man in vivo, we undertook hyperinsulinemic euglycemic clamps and measured PPAR mRNA levels and mRNA levels of lipid regulating PPAR response genes in skeletal muscle biopsies. mRNA levels were measured in 16 men, using a novel highly sensitive and specific medium throughput quantitative competitive PCR that allows reproducible measurement of multiple candidate mRNAs simultaneously. mRNA levels of PPAR were positively correlated with mRNA levels of CD36 (r = 0.77, p = 0.001), lipoprotein lipase (r = 0.54, p = 0.024), muscle type carnitine palmitoyl transferase-1 (r = 0.54, p = 0.024), uncoupling protein-2 (r = 0.63, p = 0.008) and uncoupling protein-3 (r = 0.53, p = 0.026), but not with measures of insulin sensitivity, BMI or Glut 4, which plays an important role in insulin mediated glucose uptake. Thus, our data suggest that in humans skeletal muscle PPAR expression and genes regulating lipid metabolism are tightly linked, but there was no association between both insulin sensitivity and BMI with PPAR expression in skeletal muscle.