The distinction between idiopathic dilated cardiomyopathy and myocarditis is controversial, both clinically and pathologically. To increase diagnostic accuracy and provide prognostic information, we prospectively tested the routine application of immunofluorescence and electron microscopy in endomyocardial biopsy evaluation. Biopsy samples from a consecutive series of 79 patients with cardiomyopathy and possible myocarditis were thus evaluated by light (LM), immunofluorescence (IF), and electron microscopy (EM). Patient course was followed prospectively to determine prognostic factors. Immunoglobulin (IgG) and complement (C) in biopsy tissue were graded 0 to 3+ and an IF score was derived as 2 (IgG) grade + C grade. A highly significant association was found between IF score greater than or equal to 2 and the presence of mononuclear cells (lymphocytes plus macrophages) greater than 5/high-power field, confirmed by EM; 12 of 15 (80%) with IF score greater than or equal to 2 had inflammatory cells, vs only 2 of 64 (3%) with IF score less than 2 (p less than 0.000001). EM was used to confirm the identity of infiltrating cells and to grade myofilament loss (0 to 3+) and 11 other ultrastructural features. EM did not provide important predictive information in myocarditis, but confirmed the presence of inflammatory cells. However, the EM finding of myofilament loss provided prognostic information both in patients with and without myocarditis (p less than 0.03). Mortality at 18 months was 37% for patients with 2 to 3+ myofilament loss, vs 10% in those with 0 to 1+ loss. Moreover, myofilament loss was prognostically independent of clinical class and ejection fraction. EM determination of myofilament loss is valuable as a prognostic indicator, whether or not myocarditis is present. Routine IF and EM increase the diagnostic accuracy and prognostic information in endomyocardial biopsies from patients with suspected myocarditis or cardiomyopathy.