Background Targeted therapy is now recommended for myocarditis associated with specific viruses. As such, there is increasing need for identification and typing of viral pathogens in tissue samples. Panviral capture probe-based metagenomic viral sequencing is an emerging technology that provides for the unbiased detection of potentially any pathogenic virus in a sample matrix. Herein we present a preliminary data regarding the detection of viral pathogens in formalin-fixed paraffin-embedded myocarditis specimens via metagenomic viral sequencing. Design Institutional archives were queried for cases of myocarditis (2016-2023) with age-matched controls. Cases with clinical follow-up and sufficient quantity of nucleic acid after extraction were included. In brief, formalin-fixed paraffin-embedded tissue for each case underwent total nucleic acid extraction and reverse transcription. Sample libraries were generated with dual index adaptors, and pooled indexed libraries were hybridized with viral-specific nucleic acid probes from the Comprehensive Viral Research Panel (Twist Biosciences). Post capture nucleic acid was amplified by PCR, sequenced on a NextSeq (Illumina, San Diego, CA), and analyzed with CZ-ID (czid.org; Chan-Zuckerberg Biohub). Results 14 cases (11 autopsies, 3 biopsies) with histologic myocarditis and 3 age-matched cardiac tissue controls were tested. Reads corresponding to potential viral pathogens were identified by metagenomic sequencing in 6 of 14 cases (42%) (Table 1). In one instance (Table 1; 12) the virus observed by metagenomic sequencing was confirmed by viral specific PCR. Viral metagenomic sequencing did not identify corresponding viral sequences in 2 potential cases of SARS-CoV-2 myocarditis (Table 1; 11,14) however, Cytomegalovirus (CMV) sequences were detected in one. Immunohistochemistry for CMV was negative. Three control cases were negative by metagenomic sequencing (data not shown). Conclusions Viral etiologies of myocarditis are underdiagnosed. Viral metagenomic sequencing identified a potential viral pathogen undetected by conventional clinical testing in 42% of myocarditis tissues in this pilot study. The results of this pilot are promising, but future studies are needed to characterize the utility of this testing methodology for use in detecting viral causes of myocarditis.