Hypertrophic cardiomyopathy (HCM) is a common and potentially lethal heart disease in cats. To reduce its prevalence, breeding cats are frequently screened on the basis of their phenotype or genotype. Although echocardiography is the most reliable phenotypical method, its efficacy is limited by the incomplete penetrance of HCM and by difficulties in distinguishing primary HCM from other causes of left ventricular hypertrophy. On the other hand, genetic testing is hampered by the genetic heterogeneity of the disease. Genetic tests are currently only available for Maine Coons and Ragdolls. Because of the high prevalence of HCM, stringent selection may have a negative impact on the genetic diversity of a breed. A more optimal selection would therefore be a slow and careful exclusion of phenotypically and/or genetically positive cats.