The contractile sarcomeric pool of skeletal muscle and heart consists of a highly-ordered arrangement of actin thin filaments, tropomyosin and proteins of the troponin complex: troponin I (TnI), troponin T (TnT) and troponin C (TnC). The cardiac myocyte expresses specific isoforms of both TnI and TnT (cTnI and cTnT, respectively), which can be distinguished from skeletal muscle isoforms by rapid and reliable immunoassays. Due to their superior cardiac specificity, cTnI and cTnT have become the recommended biomarkers for the diagnosis of myocardial injury. The most common applications are for risk stratification and diagnosis of acute coronary syndromes, albeit they can also be used for assessing a variety of other myocardial disorders. However, the excellent diagnostic efficiency of cardiac troponin testing is jeopardized by some pre-analytical issues (unsuitable specimens for testing, analyte stability, handling, transportation and storage of specimens prior to analysis), as well as by analytical concerns related to standardization or harmonization of cTnI immunoassays, imprecision at low concentrations, antibody specificity, immunoreactivity of plasma isoforms released in the blood after myocardial injury, interference from autoantibodies, heterophilic antibodies, rheumatoid factor, and human anti-mouse antibodies. In addition, although the influence of some known mutations in cTnT and cTnI on calcium sensitivity and force generation have been readily demonstrated, their influence on current immunoassays is unknown. Most mutations in these proteins may contribute to the development of certain cardiomyopathies, namely hypertrophic and restrictive. In these situations, the phenotype is characterized by the underlying diseases, and the ability to detect cTnT or cTnI is of relatively little clinical significance. However, the cTnT Arg129Lys polymorphism and those observed in the stable domain of cTnI do not significantly alter the functional properties of the molecule within the myocardium and thus are predictably asymptomatic. While the actual prevalence of these polymorphisms in the general population is still unknown, they might be a source of potential analytical problems; modifying the immunogenicity of the molecule and leading to potential false negative results. The goal of this article is to provide an overview on the potential technical and analytical challenges in the measurement of cardiac troponins, along with the significance of polymorphisms in the genes encoding for cTnI and cTnT in both health and disease. Clin Chem Lab Med 2009;47:1183–94.