Myocarditis. Lymphocytic myocarditis is the most common form of myocarditis in Western countries, and most of the cases are documented or presumed to be viral in origin. Nonviral infective agents are exceptional and often morphologically distinctive and identifiable by routine histology also including special stains. On the contrary, Classical morphological analysis (histology and immunohistochemistry) has great limits in the detection of viral agents and usually lacks specific cytopathic features, with the rare exception of some forms, like cytomegalovirus (CMV) myocarditis. The development of molecular biological techniques, particularly amplification methods such as polymerase chain reaction (PCR), allows the detection of low copy of viral genomes even from an extremely small amount of tissue such as endomyocardial biopsy. PCR is an enzymatic amplification technique whereby very few copies of RNA or DNA sequences can be amplified more than a millionfold. This allows transformation of a target sequence (i.e., the pathogen in question) from very low numbers to literally millions of copies without cloning technology. The main viruses to be considered when performing molecular pathology studies in the myocardium of patients with a suspicion of myocarditis are adenovirus, CMV, Epstein-Barr virus (EBV), enterovirus, hepatitis C virus, Human Herpes Virus 6 (HHV6), herpes simplex viruses 1 and 2, influenza viruses A and B, and Parvovirus B19 (PVB19). Other infectious agents may be investigated according to the clinical indication (Table 11.1) (Fig. 11.1) [5–7]. However, it has been underlined that the presence of viral genomes does not automatically imply a direct role of viruses in the pathogenesis of myocarditis, since an infective agent detected by PCR/RT-PCR/nested-PCR may be just an innocent bystander. Therefore, it is recommended to use molecular techniques as diagnostic tools ancillary to other mandatory investigations, either clinical or morphological, and apply it with skilled expertise. Positive PCR results obtained on the myocardial samples should always be accompanied by a parallel investigation on blood samples and/or frozen spleen. The absence of a viral genome in the blood and/or spleen sample rules out the possibility of passive blood contamination of the myocardium, while viral blood positivity requires additional investigation by using quantitative PCR analysis. Among the molecular biology techniques used to differentiate viral genomes, gene sequencing allows not only the precise characterization of the infective agent but also can help in assessing the molecular basis of cardiotropism as well as cardiovirulence. Finally, more recently the need of viral genome load quantification has been advanced particularly for some viruses such as PVB19, which are frequently encountered in the diagnostic workup not only of myocarditis but also of healthy transplant donor, of autoptic samples without myocarditis or with borderline myocarditis, and of patients undergoing endomyocardial biopsy for other reasons.