Heart disease is the leading health problem of industrialized countries. The development of gene therapies tailored towards the heart has grown exponentially over the past decade. Murine models of heart diseases have played a pivotal role in testing novel cardiac gene therapy approaches. Unfortunately, the small body size and rapid heart rate of mice present a great challenge to heart function evaluation. Here we outline the commonly used cardiac phenotyping methods of treadmill exercise regimen, full 12-lead electrocardiographic assay and left ventricular catheterization hemodynamic assay. Application of these protocols will allow critical testing of gene therapy efficacy in mouse models of heart diseases.