Polymorphisms in the CYP2C9 gene can have a significant impact on drug therapy by affecting the pharmacokinetics of frequently prescribed drugs, such as phenprocoumon and warfarin. It is essential therefore that genetic CYP2C9 variants are excluded in patients with a suspected intolerance of anticoagulant therapy. Here we present the first report of a case of left ventricular non-compaction syndrome associated with a genetic variant of the CYP2C9 gene in a 45-year-old woman with myocardial insufficiency who was scheduled for implantation of a cardioverter defibrillator.