Recently, proteome analysis has been introduced to analyze differential protein expression and cellular protein composition in cardiovascular medicine. Proteins expressed by diseased hearts (myocardial proteomics) were first investigated over a decade ago using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). However, while 2D-PAGE is very successful for the abundant and moderately expressed proteins, it struggles to identify proteins expressed at low levels. However, the sensitivity of mass spectrometry has increased considerably during recent years, and technical progress widens the detection limits of mass-spectrometric analysis. Proteomics now allows us to examine global alterations in protein expression in the diseased hearts, and will provide new insights into the cellular mechanisms involved in cardiac dysfunction. This review will summarize the present knowledge about the use of proteome analysis in myocardial diseases.