Endomyocardial biopsy (EMB) is often performed in patients presenting with sudden onset of heart failure to identify myocarditis. The introduction of immunohistochemical techniques for the detection and differentiation of infiltrating immune cells, specific adhesion molecules and MHC class I and II molecules increased the prognostic value of EMB in the diagnosis of myocarditis considerably. A major breakthrough in the understanding of pathogenetic mechanisms in myocarditis was achieved by diagnostic use of molecular biological methods. By application of in situ hybridization and PCR, enteroviruses, and more recently, parvovirus B19 (PVB19) have been identified as relevant agents of myocarditis. The different cell tropism of these viruses implicates distinct pathogenic principles, which, at present, are not completely understood. Whereas enteroviruses damage the heart primarily via direct lysis of infected myocytes, PVB19 does not infect myocytes, but endothelial cells of small intracardiac arterioles and venules, resulting in impairment of myocardial microcirculation with secondary myocyte necrosis during acute infection. Histological and immunohistological stainings combined with molecular biological approaches in EMB will help us to resolve the question of whether patients with myocarditis should be treated by specific antiviral agents or by immunosuppressive therapies.