Expression and localization of proteins in tissue determines anatomy and physiology, and thus provides a clue to pathology. However, it is strenuous to identify the expression and localization of multiple targets using conventional immunostaining technique, especially when there is no specific antibody, nor explicit assumption, for target proteins. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry is a proteomic technique to simultaneously map multiple targets in a frozen tissue section. Using this technique, we analyzed protein expression in heart, and in testis as a reference sample, in 129/sv mice. Spatial distribution of at least 57 individual proteins was simultaneously identified at 100 um resolution. Among them, cardiac alpha actin, cardiac troponin T, tropomyosin alpha-1 chain, titin, myosin light chain 1 (MYL1), myosin light chain 3 (MYL3), myosin-6 were exclusively expressed in the heart. MYL1 and MYL3, the altered expression of which is associated with heart failure, were localized in the atrium and in the ventricle, respectively, as expected. Interestingly, protein expression profile of cysteine-rich protein 2 and myomesin-1 is exactly as predicted from mRNA expression, namely more in the heart and less in the testis. Expression level of housekeeping genes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and beta actin, was similar between the heart and the testis. These results suggest that MALDI imaging may provide a new platform for analysis of pathology and subsequent application to diagnosis of heart diseases.