The evaluation of myocardial damage in relation to cardiac operation from a clinical and a research perspective is of great importance, particularly for the evaluation of different cardioprotective strategies. Although measurements of serum biochemical markers have often been used, their value has been limited by their lack of sensitivity and specificity in the presence of skeletal muscle damage. A newer range of markers are now available that may reliably indicate both perioperative myocardial infarction, as well as more subtle degrees of subclinical myocyte injury. In this review, the application of biochemical markers for clinical and research purposes during cardiac operation is considered.