Myocardial diseases are often encountered in cardiology and pose a significant diagnostic challenge. Myocarditis is an acute inflammatory disease of the heart muscle. Pathophysiology of myocarditis is a complex interplay of genetic background, innate immunity, viral or bacterial agents and formation of autoreactive antibodies and lymphocytes that maintain the inflammation after the infection was eliminated. Differentiation of myocardial infarction or heart failure of different etiology is crucial in the acute stage. Cardiac magnetic resonance imaging (MRI) enables with sufficient sensitivity and specificity diagnosis of myocardial inflammation and scar. Endomyocardial biopsy (EMB) with histology and immunohistochemistry is a gold standard for detection of myocarditis. EMB is indicated in selected patients with life-threatening symptoms where EMB may have therapeutic consequences. Giant cell myocarditis and eosinophilic myocarditis are specific examples of such a condition. Polymerase chain reaction (PCR) of the myocardial sample is used to detect viral genome. Serum antibodies or PCR from blood are not helpful in determining the etiology of myocarditis. Viral presence in myocardium is found in patients who do not have histological evidence of myocarditis which makes the association of positive PCR and etiology of myocarditis obscure. Cardiomyopathies (CMP) are characterized by structural and functional cardiac abnormalities that cannot be explained by coronary artery disease or abnormal loading conditions (valvular disease, arterial hypertension, congenital heart disease). CMP are classified based on the prevailing morphology regardless of primary (genetic, idiopathic) or secondary (systemic disease) etiology. European Society of Cardiology defines five types of CMP: hypertrophic, dilated, restrictive, arrhythmogenic and unclassified. CMP diagnosis is based on the imaging with echocardiography, coronary angiography, invasive hemodynamics and cardiac MRI. EMB is rarely indicated in dilated or restrictive CMP. Genetic testing is used to determine pathogenic mutations in phenotype positive patients and in familiar screening. Genetically determined CMP are mostly monogenic and autosomal dominant. Incomplete penetrance and variable expressivity cause variable or even negative phenotypes in genotype positive individuals. Genetic screening of a large number of genes and non-coding DNA results in findings of many variants of uncertain significance which make the interpretation of the genetic testing difficult.

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