Arterial hypertension is the most frequent chronic disease and it is an important cause of morbidity and mortality in the developed world. Arterial hypertension is associated with such adverse effects as accelerated arteriosclerosis and pathological left ventricular hypertrophy, among others. The molecular mechanisms affecting left ventricular hypertrophy remain mostly unknown. The advent of proteome profiling has facilitated the elucidation of disease-associated proteins, paving the way for molecular diagnostics and the identification of novel therapeutic targets. We explored the proteomic profile of pathological left ventricular hypertrophy in comparison with normal heart in a model of rats and investigated the proteomic changes in response to different antihypertensive regimens in order to elucidate their cardioprotective effects. Here we describe in depth the protocol for this type of study.