Imaging of tissue sections by mass spectrometry provides a detailed molecular picture containing information on both the abundance and distribution of many constituent compounds. Mass spectra are acquired directly from fresh frozen tissue sections using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS); sample preparation and data collection mode determine the spatial resolution or surface area of the section represented in each mass spectrum. Statistical analyses of the individual ion signatures yield biomarkers whose abundances correlate to cell development processes, tumorigenesis and/or drug treatment. In an alternate mode, the generation of intensity maps for individual ions provides a visual representation of the distribution of each species throughout the section at spatial resolutions as small as 50 microm. The availability of this molecular information is likely to be of great value to clinicians and should lead to improved therapeutic efficacy in the future.