Previous studies have shown that matrix-assisted laser desorption/ionization–imaging mass spectrometry (MALDI-IMS) is useful for studying the distribution of various small metabolites, particularly lipids. However, in this technique, selective ionization of the target molecules is imperative, particularly when analyzing small molecules. Since the sample clean-up procedures available for the MALDI-IMS of small metabolites are limited, the tissue sample will contain numerous molecular species other than the target molecules. These molecules will compete for ionization resulting in severe ion suppression. Hence, it is necessary to develop and optimize a sample preparation protocol for the target molecules. In this study, through model experiments using reference compounds, we optimized the composition of the matrix solution used for positively charged lipids in terms of the concentration of the organic solvent and presence/absence of alkali metal salts. We demonstrated that a high concentration of organic solvent in the matrix solution favors the preferential detection of lipids over peptides. The presence of alkali metal salts in the matrix solution was favorable for the detection of polar lipids, while a salt-free matrix solution was suitable for the detection of nonpolar lipids. Furthermore, potassium salts added to the matrix solution caused merging of various lipid adducts (adducts with proton, sodium, and potassium) into one single potassiated species. Using the optimized protocols, we selectively analyzed phosphatidylcholine (PC) and triacylglycerol (TG) with different fatty acid compositions in a rat kidney section. Copyright © 2009 John Wiley & Sons, Ltd.