Hypertrophic cardiomyopathy (HCM) is the most common feline heart disease and an important health concern. While many affected cats can survive to advanced age, HCM is associated with substantial morbidity and premature cardiac death. In humans HCM has an established heritable basis with thousands of identified mutations; however, the mutation is usually unknown in feline HCM. Disease penetrance is variable, expression of left ventricular hypertrophy varies from focal to diffuse chamber involvement, and clinical signs range from subclinical to heart failure and sudden death. The molecular mechanism and triggers that affect HCM phenotype are unresolved, although modifiable metabolic and/or dietary factors are hypothesized to modulate the expression of hypertrophy. Identifying related environmental modulators could help improve our understanding of mechanisms related to risk identification and facilitate development of clinical tests to predict progression. Metabolomics, the high-throughput study of the soluble metabolites associated with physiologic state, has the potential to accelerate the identification of novel HCM-biomarkers for risk identification.