CPT I (outer membrane carnitine palmitoyltransferase I) is a crucial enzyme in myocardial substrate selection. Two isoforms exist in the heart, the liver (L-) and muscle (M-) isoforms, which have different kinetic characteristics and alter in relative amounts during the neonatal/weaning/adult transition. CPT I is a point for control and regulation of fatty acid oxidation via modulation of its activity by malonyl-CoA, the concentration of which is set by acetyl-CoA carboxylase, AMP-activated protein kinase and malonyl-CoA decarboxylase in response to, for example, alterations in glucose supply. Systemic inflammatory responses and sepsis lead to myocardial dysfunction as part of multiple system organ failure. We have shown that: (i) myocardial CPT I activity is inhibited during neonatal sepsis; (ii) on the basis of inhibitor studies this inhibition appears to be of M-CPT I rather than L-CPT I; (iii) nitration of M-CPT I occurs, probably by peroxynitrite, and this may be responsible for the decrease in CPT I activity; (iv) myocardial CPT I activity is also inhibited in another model of systemic inflammatory response, namely intestinal ischaemia/reperfusion injury, but this can prevented by whole-body moderate hypothermia. Inhibition of M-CPT I would be predicted to alter myocardial substrate selection but there are several questions that remain to be answered.