We report the association of eosinophilic esophagitis (EoE) and hypertrophic cardiomyopathy (HCM) and provide genetic data indicating a linkage between EoE and HCM. The letter begins with an index patient diagnosed with both EoE and HCM and found to have a known genetic mutation for HCM. We then identify an odds ratio of nearly 8 for having both EoE and HCM following review of an electronic medical record with >1,000,000 individuals. Finally, via a candidate gene approach we identify significant association of HCM gene variants in a cohort of EoE patients versus control subjects. Collectively, we have identified a putative interaction between EoE and HCM with clinical and pathogenic implications.